Develop Reference

mambaforge, conda executable path is empty in pycharm interpreter(Linux mint 20)

I have installed conda environment using mambaforge to use snakemake. I have followed the instructions of Snakemake setup tutorial to install mambaforge. I have created the environment and created a .py file, but when I try to run it, it shows the plain code rather than compiling it. When I went to fix it and to add a Conda environment in my PyCharm interpreter it shows me the following error:
I tried to add the conda executable path by browsing to mambaforge/bin/conda but it still shows me the error.
I also tried to use which conda to find the right path, but rather than giving me a path the following is show, I have tried which conda in conda base environment as well as my setup environment, all it returns is the following:
I am sure that my conda environment is setup as conda --version command shows me the version I have installed.

the conda bin installed with mambaforge is at ~/mambaforge/condabin/conda

I'm not aware of mambaforge conda distribution, I'm using Anaconda / Miniconda distributions with an installed mamba module, so I could create a snakemake environment using terminal (i.e. from command line) and register as Python interpreter in PyCharm Settings as "Conda Environment | Existing environment" (see your first screenshot).
So I suggest you:
check whether "Existing environment" works for you, e.g. is able to find you conda environments (e.g base, or others).
You could set up Anaconda/Miniconda + mamba + configure PyCharm for using Snakemake with the help of my detailed guide that I use for my students' homework on snakemake.
P.S: I always run snakemake scripts using command line, e.g from terminal bundled into PyCharm, or just system terminal app or on remote server. I don't use PyCharm run configurations for that. As for PyCharm, I use it with SnakeCharm plugin to have a good snakemake & python code editing support

Anaconda will not run

I've installed Anaconda 3, version 2020.02 (current version straight from the website, 64 bit), and cannot figure out how to run it. When I search (on Windows) for Anaconda prompt or Anaconda navigator, I cannot find either. When I try to run any commands like conda init or anaconda-navigator on the command line, it says 'conda is not recognized as an internal or external command'. Yet it did install successfully (supposedly); the installed Anaconda3 files are where they should be. I have added the proper filepath to my system PATH variable, and added Anaconda3/Scripts to the PATH variable as well; neither of these make a difference. Typing 'where conda' on command line results in 'INFO: Could not find files for the given patterns'. I have uninstalled Anaconda and reinstalled an earlier version, and this does not work either. What next steps should I take to try to get Anaconda to run?

Install Anaconda and don't change any of the default settings. This will install Anaconda in your user profile and add the c:\users\user_name\AppData\Anaconda3\condabin folder to your system path. But before you can actually use Anaconda, you'll need to activate an environment. Either use the Anaconda prompt shortcut or open a cmd shell and type conda activate. If the the prompt doesn't change to (base) C:\users\user_name> Anaconda won't work. Adding ../Anaconda3/Scripts to the PATH simply isn't sufficient. If necessary go to the c:\users\user_name\AppData\Anaconda3\condabin folder and run conda init again.

Changing default conda environment [duplicate]

I've installed Anaconda and created two extra environments: py3k (which holds Python 3.3) and py34 (which holds Python 3.4). Besides those, I have a default environment named 'root' which the Anaconda installer created by default and which holds Python 2.7. This last one is the default, whenever I launch 'ipython' from the terminal it gives me version 2.7. In order to work with Python 3.4, I need to issue the commands (in the shell)
source activate py34
ipython
which change the default environment to Python 3.4. This works fine, but it's annoying since most of the time I work on Python 3.4, instead of Python 2.7 (which I hold for teaching purposes, it's a rather long story). Anyway, I'll like to know how to change the default environment to Python 3.4, bearing in mind that I don't want to reinstall everything from scratch.

If you just want to temporarily change to another environment, use
source activate environment-name
ETA: This may be deprecated. I believe the current correct command is:
source conda activate environment-name
(you can create environment-name with conda create)
To change permanently, there is no method except creating a startup script that runs the above code.
Typically it's best to just create new environments. However, if you really want to change the Python version in the default environment, you can do so as follows:
First, make sure you have the latest version of conda by running
conda update conda
Then run
conda install python=3.5
This will attempt to update all your packages in your root environment to Python 3 versions. If it is not possible (e.g., because some package is not built for Python 3.5), it will give you an error message indicating which package(s) caused the issue.
If you installed packages with pip, you'll have to reinstall them.

Overview
Some people have multiple Conda environments with different versions of Python for compatibility reasons. In this case, you should activate the desired default environment in the shell initialization file (e.g., .bashrc, .zshrc). With this method, you can preserve the versions of Python you use in your environments.
The following assumes environment_name is the name of your environment
Mac / Linux:
Edit your bash profile so that the last line is conda activate environment_name. In Mac OSX this is ~/.bash_profile, in other environments this may be ~/.bashrc
Example:
Here's how I did it on Mac OSX
Open Terminal and type:
nano ~/.bash_profile
Go to end of file and type the following, where "p3.5" is my environment:
conda activate p3.5
Exit File. Start a new terminal window.
Type the following to see what environment is active
conda info -e
The result shows that I'm using my p3.5 environment by default.
For Windows:
Create a command file (.cmd) with activate environment_name and follow these instructions to have it execute whenever you open a command prompt
Create a batch file command, e.g. "my_conda.cmd", put it in the Application Data folder.
Configure it to be started automatically whenever you open cmd. This setting is in Registry:
key: HKCU\SOFTWARE\Microsoft\Command Processor
value: AutoRun
type: REG_EXPAND_SZ
data: "%AppData%\my_conda.cmd"
from this answer: https://superuser.com/a/302553/143794

Under Linux there is an easier way to set the default environment by modifying ~/.bashrc or ~/.bash_profile
At the end you'll find something like
# added by Anaconda 2.1.0 installer
export PATH="~/anaconda/bin:$PATH"
Replace it with
# set python3 as default
export PATH="~/anaconda/envs/python3/bin:$PATH"
and thats all there is to it.

For windows Anaconda comes with Anaconda Prompt which is a shortcut to cmd and can be used run conda commands without adding anaconda in PATH variable.
Find the location of it, copy and rename the copy (say myenv_prompt). Right click myenv_prompt and select properties in the context menu.
The Target form of Properties window should already be filled with text, something like %windir%\system32\cmd.exe "/K" C:\Users\xxx\AppData\Local\Continuum\Miniconda3\Scripts\activate.bat C:\Users\xxx\AppData\Local\Continuum\Miniconda3\
There are three parts of this command 1)start ...\cmd.exe 2)run ...\acitvate.bat with environment 3)...\Miniconda3\
Change 3rd part to path of the environment (say myenv) you want as default i.e. fill the Target form something like %windir%\system32\cmd.exe "/K" C:\Users\xxx\AppData\Local\Continuum\Miniconda3\Scripts\activate.bat C:\Users\xxx\AppData\Local\Continuum\Miniconda3\envs\myenv
Now myenv_prompt will act as shortcut to start cmd with myenv as the default environment for python. This shortcut you can keep in start menu or pinned in taskbar.
One advantage of this method is that you can create a few shortcuts each having different environment as default environment. Also you can set the default folder by filling Start in form of the Properties window
Hope this helps
PS:It is not required to find Anaconda Prompt and can be done by changing target of any shortcut. But you will require to know path of cmd.exe and activate.bat

Just activate your py34 environment when you load your terminal/shell.
If you use Bash, put the line:
conda activate py34
in your .bash_profile (or .bashrc):
$ echo 'conda activate py34' >> ~/.bash_profile
Every time you run a new terminal, conda environment py34 will be loaded.

The correct answer (as of Dec 2018) is... you can't. Upgrading conda install python=3.6 may work, but it might not if you have packages that are necessary, but cannot be uninstalled.
Anaconda uses a default environment named base and you cannot create a new (e.g. python 3.6) environment with the same name. This is intentional. If you want your base Anaconda to be python 3.6, the right way to do this is to install Anaconda for python 3.6. As a package manager, the goal of Anaconda is to make different environments encapsulated, hence why you must source activate into them and why you can't just quietly switch the base package at will as this could lead to many issues on production systems.

Change permanent
conda install python={version}
Change Temporarily
View your environments
run conda info --envs on your terminal window or an Anconda Prompt
If It doesn't show environment that you want to install
run conda create -n py36 python=3.6 anaconda for python 3.6 change version as your prefer
Activating an environment (use Anaconda prompt)
run activate envnme envnme you can find by this commandconda info --envs as a example when you run conda info --envs it show
base * C:\Users\DulangaHeshan\Anaconda3
py36 C:\Users\DulangaHeshan\Anaconda3\envs\py36
then run activate py36
to check run python --version
In Windows, it is good practice to deactivate one environment before activating another.
https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html?highlight=deactivate%20environment

If you want Anaconda Navigator to default to Virtual Env you created, go to file > Preference and select default conda env in drop down lint:
If you want Anaconda command automatically opens to virtual env without having to type activate envName, do this:
Right click on conda shortcut > go to properties and change the Target to something like this:
%windir%\System32\cmd.exe "/K" C:\Anaconda\Scripts\activate.bat C:\Anaconda\envs\p37
Optionally you can set your default working dir as well, like I did in snapshop below:
gl

On Windows, create a batch file with the following line in it:
start cmd /k "C:\Anaconda3\Scripts\activate.bat C:\Anaconda3 & activate env"
The first path contained in quotes is the path to the activate.bat file in the Anaconda installation. The path on your system might be different. The name following the activate command of course should be your desired environment name.
Then run the batch file when you need to open an Anaconda prompt.

Here is the solution I found for autoactivating my preferred environment on a Windows 10 system:
Open anaconda prompt & use 'conda env list' to find the location of the environment you wish to use.
Go to the start menu, right-click 'Anaconda Prompt' and go to file location.
Create a copy of this shortcut file
Open its properties & change the target to the location of your preferred environment.
Now every time you open anaconda prompt through this shortcut it will automatically load your chosen environment.

activate.py is hardcoded to emit conda activate base\n into your shell profile when you evaluate the shell hook produced by conda shell.zsh hook.
you can suppress this hardcoded "auto-activate base" via:
conda config --set auto_activate_base false
then, in ~/.zshrc, ~/.bashrc or wherever you source your shell profile from, you can append the following (after the conda shell hook) to explicitly activate the environment of your choosing:
conda activate py34

I wasn't satisfied with any of the answers presented here, since activating an environment takes a few seconds on my platform (for whatever reason)
I modified my path variable so that the environment I want as default has priority over the actual default.
In my case I used the following commands to accomplish that for the environment "py35":
setx PATH "%userprofile%\Anaconda3\envs\py35\;%PATH%"
setx PATH "%userprofile%\Anaconda3\envs\py35\Scripts;%PATH%"
to find out where your environment is stored, activate it and enter where python.
I'm not sure yet if this approach has any downsides. Since it also changes the default path of the conda executable. If that should be the case, please comment.

For Jupyter and Windows users, you can change the Target path in your Jupyter Notebook (anaconda3) shortcut from C:\Users\<YourUserName>\anaconda3 to C:\Users\<YourUserName>\anaconda3\envs\<YourEnvironmentName>
you could do the same thing for the Anaconda Prompt..etc.
After changing the path you can check your active environment by opening a terminal in Jupyter and run conda info --envs.

I got this when installing a library using anaconda. My version went from Python 3.* to 2.7 and a lot of my stuff stopped working.
The best solution I found was to first see the most recent version available:
conda search python
Then update to the version you want:
conda install python=3.*.*
Source: http://chris35wills.github.io/conda_python_version/
Other helpful commands:
conda info
python --version

Create a shortcut of anaconda prompt onto desktop or taskbar, and then in the properties of that shortcut make sure u modify the last path in "Target:" to the path of ur environment:
C:\Users\BenBouali\Anaconda3\ WILL CHANGE INTO
C:\Users\BenBouali\Anaconda3\envs\tensorflow-gpu
preview
and this way u can use that shortcut to open a certain environment when clicking it, you can add it to ur path too and now you'll be able to run it from windows run box by just typing in the name of the shortcut.

Tried both source activate default_3_9 and source conda activate default_3_9
but worked conda activate default_3_9

I'm trying to update Anaconda in order to use Python 3.10.4 and then Spyder 5.3.2. Actually, I wanted to set the Python interpreter used by Pycharm inside the Spyder console but it required the newest Spyder version. I didn't try all the possible solutions (it's pending for me to use the window batch and modifying path solutions given here) but:
Since I couldn't update the Anaconda base due to the well-known error on the "Solving environment". Then Python and Spyder remain the same.
Creating a new env allows to get the last Python and then his newest Spyder version but it doesn't actualize the Anaconda shortcuts and even the Anaconda navigator if you set it to this new env still has some inconsistencies like keeping the older Spyder version in his menu.
Besides, on point 2, changing the shortcuts target path doesn't work for me.
Finally, I create a new shortcut of the Spyder file from the Scripts folder inside the environment directory ( C:\Users<userName>>\Anaconda3\envs<EnvName>\Scripts )
I couldn't use the default Anaconda shortcuts but I have what I wanted and quick access.

'Conda' is not recognized as internal or external command

I installed Anaconda3 4.4.0 (32 bit) on my Windows 7 Professional machine and imported NumPy and Pandas on Jupyter notebook so I assume Python was installed correctly. But when I type conda list and conda --version in command prompt, it says conda is not recognized as internal or external command.
I have set environment variable for Anaconda3; Variable Name: Path, Variable Value: C:\Users\dipanwita.neogy\Anaconda3
How do I make it work?

I was faced with the same issue in windows 10, Updating the environment variable following steps, it's working fine.
I know It is a lengthy answer for the simple environment setups, I thought it's may be useful for the new window 10 users.
1) Open Anaconda Prompt:
2) Check Conda Installed Location.
where conda
3) Open Advanced System Settings
4) Click on Environment Variables
5) Edit Path
6) Add New Path
C:\Users\RajaRama\Anaconda3\Scripts
C:\Users\RajaRama\Anaconda3
C:\Users\RajaRama\Anaconda3\Library\bin
7) Open Command Prompt and Check Versions
8) After 7th step type
conda install anaconda-navigator in cmd then press y

Although you were offered a good solution by others I think it is helpful to point out what is really happening. As per the Anaconda 4.4 changelog, https://docs.anaconda.com/anaconda/reference/release-notes/#what-s-new-in-anaconda-4-4:
On Windows, the PATH environment variable is no longer changed by default, as this can cause trouble with other software. The recommended approach is to instead use Anaconda Navigator or the Anaconda Command Prompt (located in the Start Menu under “Anaconda”) when you wish to use Anaconda software.
(Note: recent Win 10 does not assume you have privileges to install or update. If the command fails, right-click on the Anaconda Command Prompt, choose "More", chose "Run as administrator")
This is a change from previous installations. It is suggested to use Navigator or the Anaconda Prompt although you can always add it to your PATH as well. During the install the box to add Anaconda to the PATH is now unchecked but you can select it.

I found the solution.
Variable value should be C:\Users\dipanwita.neogy\Anaconda3\Scripts

When you install anaconda on windows now, it doesn't automatically add Python or Conda to your path.
While during the installation process you can check this box, you can also add python and/or python to your path manually (as you can see below the image)
If you don’t know where your conda and/or python is, you type the following commands into your anaconda prompt
where python
where conda
Next, you can add Python and Conda to your path by using the setx command in your command prompt (replace C:\Users\mgalarnyk\Anaconda2 with the results you got when running where python and where conda).
SETX PATH "%PATH%;C:\Users\mgalarnyk\Anaconda2\Scripts;C:\Users\mgalarnyk\Anaconda2"
Next close that command prompt and open a new one. Congrats you can now use conda and python
Source: https://medium.com/#GalarnykMichael/install-python-on-windows-anaconda-c63c7c3d1444

Just to be clear, you need to go to the controlpanel\System\Advanced system settings\Environment Variables\Path,
then hit edit and add:
C:Users\user.user\Anaconda3\Scripts
to the end and restart the cmd line

In addition to adding C:\Users\yourusername\Anaconda3 and C:\Users\yourusername\Anaconda3\Scripts, as recommended by Raja (above), also add C:\Users\yourusername\Anaconda3\Library\bin to your path variable. This will prevent an SSL error that is bound to happen if you're performing this on a fresh install of Anaconda.

If you have a newer version of the Anaconda Navigator, open the Anaconda Prompt program that came in the install. Type all the usual conda update/conda install commands there.
I think the answers above explain this, but I could have used a very simple instruction like this. Perhaps it will help others.

Go To anaconda prompt(type "anaconda" in search box in your laptop). type following commands
where conda
add that location to your environment path variables. Close the cmd and open it again

This problem arose for me when I installed Anaconda multiple times. I was careful to do an uninstall but there are some things that the uninstall process doesn't undo.
In my case, I needed to remove a file Microsoft.PowerShell_profile.ps1 from ~\Documents\WindowsPowerShell\. I identified that this file was the culprit by opening it in a text editor. I saw that it referenced the old installation location C:\Anaconda3\.

For conda --version greater than 4.6, from the base of your Anaconda promt, run
conda update conda
conda init
This will update your conda root environment and setup the stuff you need to run it on both cwd and powershell.
After this, you can start any terminal and it will be conda ready.

If you don't want to add Anaconda to env. path and you are using Windows try this:
Open cmd;
Type path to your folder instalation. It's something like:
C:\Users\your_home folder\Anaconda3\Scripts
Test Anaconda, for exemple type conda --version.
Update Anaconda: conda update conda or conda update --all or conda update anaconda.
Update Spyder:
conda update qt pyqt
conda update spyder

I have Windows 10 64 bit, this worked for me,
This solution can work for both (Anaconda/MiniConda) distributions.
First of all try to uninstall anaconda/miniconda which is causing problem.
After that delete '.anaconda' and '.conda' folders from 'C:\Users\'
If you have any antivirus software installed then try to exclude all the folders,subfolders inside 'C:\ProgramData\Anaconda3\' from
Behaviour detection.
Virus detection.
DNA scan.
Suspicious files scan.
Any other virus protection mode.
*(Note: 'C:\ProgramData\Anaconda3' this folder is default installation folder, you can change it just replace your excluded path at installation destination prompt while installing Anaconda)*
Now install Anaconda with admin privileges.
Set the installation path as 'C:\ProgramData\Anaconda3' or you can specify your custom path just remember it should not contain any white space and it should be excluded from virus detection.
At Advanced Installation Options you can check "Add Anaconda to my PATH environment variable(optional)" and "Register Anaconda as my default Python 3.6"
Install it with further default settings. Click on finish after done.
Restart your computer.
Now open Command prompt or Anaconda prompt and check installation using following command
conda list
If you get any package list then the anaconda/miniconda is successfully installed.

I have just launched anaconda-navigator and run the conda commands from there.

For those who didn't check "Add Anaconda to my PATH environment variable". In Windows 10 it looks like that:
5 paths:
C:\Users\shtosh\anaconda3
C:\Users\shtosh\anaconda3\Library\mingw-w64\bin
C:\Users\shtosh\anaconda3\Library\usr\bin
C:\Users\shtosh\anaconda3\Library\bin
C:\Users\shtosh\anaconda3\Scripts

if you use chocolatey, conda is in C:\tools\Anaconda3\Scripts

I had this problem in windows. Most of the answers are not as recommended by anaconda, you should not add the path to the environment variables as it can break other things. Instead you should use anaconda prompt as mentioned in the top answer.
However, this may also break. In this case right click on the shortcut, go to shortcut tab, and the target value should read something like:
%windir%\System32\cmd.exe "/K" C:\Users\myUser\Anaconda3\Scripts\activate.bat C:\Users\myUser\Anaconda3

Anaconda3 2.4 with python 3.5 installation error (procedure entry not found; Windows 10)

I have just made up my mind to change from python 2.7 to python 3.5 and therefore tried to reinstall Anaconda (64 bit) with the 3.5 environment. When I try to install the package I get several errors in the form of (translation from German, so maybe not exact):
The procedure entry "__telemetry_main_return_trigger" could not be found in the DLL "C:\Anaconda3\pythonw.exe".
and
The procedure entry "__telemetry_main_invoke_trigger" could not be found in the DLL "C:\Anaconda3\python35.dll".
The title of the second error message box still points to pythonw.exe. Both errors appear several times - every time an extraction was completed. The installation progress box reads
[...]
extraction complete.
Execute: "C:\Anaconda3\pythonw.exe" "C:\Anaconda3\Lib_nsis.py" postpkg
After torturing myself through the installation I get the warning
Failed to create Anaconda menus
If I ignore it once gives me my lovely error messages and tells me that
Failed to initialize Anaconda directories
then
Failed to add Anaconda to the system PATH
Of course nothing works, if I dare to use this mess it installs. What might go wrong? On other computers with Windows 10 it works well.
P.S.: An installation of Anaconda2 2.4 with python 2.7 works without any error message, but still is not able to be used (other errors).

Finally I have found the reason. So, if anybody else has this problem:
Here the entry points are an issue as well and Michael Sarahan gives the solution. Install the Visual C++ Redistributable for Visual Studio 2015, which is used by the new version of python, first. After that install the Anaconda-package and it should work like a charm.

You can also use your standard Anaconda installation and just create an environment based on 2.7 / 3.4 etc... Anaconda will download and install all compatible packages from the repository so you have a complete installation.
conda create -n py27 python=2.7 anaconda
conda create -n py34 python=3.4 anaconda
To use the new environment (in Windows), you can point your IDE to the required environment folder:
C:\Anaconda3\envs\py34\python.exe
On the Windows command line, you just need to type:
activate py34
Documentation:
http://conda.pydata.org/docs/py2or3.html
My recommendation would be to reinstall your Anaconda version with Python 2.7 that you previously had working, then just add a new environment for Python 3.x and use that as you need.

I had the same problem, then I Installed "for all users": solved.
Much easier than the links provided for a beginner as I am.

For the problem "Failed to create Anaconda menus", it may because:
This might happen if PATH is too long already. How long is your PATH environment variable? Windows limits this to 1024 characters. There are some workarounds go shorten it here: How do you avoid over-populating the PATH Environment Variable in Windows?
This is other people's question and solution
https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/mjrbE6rKyi8
When I shorted the environment path, it works!

If you are getting errors like:
Failed to create Anaconda menus
Failed to initialize Anaconda directories
Failed to add Anaconda to the system PATH
just ignore them while installation and when installation is done look for the directory "anaconda3" is installed and correct the path accordingly in environment variables path.
In my system, path was set "C:\Anaconda3" but actually it was installed at "C:\ProgramData\Anaconda3". You have to change all 3 path entries for anaconda3 and then try to run "jupyter notebook" in CMD.

If you are using windows, launch the command prompt as administrator and execute the following commands
"C:\ProgramData\Anaconda3\pythonw.exe" -E -s "C:\ProgramData\Anaconda3\Lib_nsis.py" addpath
"C:\ProgramData\Anaconda3\pythonw.exe" -E -s "C:\ProgramData\Anaconda3\Lib_nsis.py" mkdirs
"C:\ProgramData\Anaconda3\pythonw.exe" -E -s "C:\ProgramData\Anaconda3\Lib_nsis.py" mkmenus
Don't forget to change the path to the path in your system. Before running this commands there will not be any Anaconda Navigator app in your start menu. After executing this commands make sure Anaconda Navigator app is available in the start menu.

Change the directory. It works
C:\miniconda3