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user is prompted for miniconda even if anaconda already present #607
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This was by design (although perhaps we can still reconsider). Our intention was that, unless the user has explicitly requested a particular version of Python with one of the Note that you will only be prompted once, and rejecting that prompt is "sticky" (you won't get bugged about it again on the same account / machine) |
I see. Thanks for the clarification ! I guess I should always use I guess it just feels unexpected when you already have anaconda configured to get advice to download the little brother miniconda. I would have considered to be prompted if no Python was found or if on windows not a python with conda. |
Our idea is that by standardizing on a known variant of Python we'll make
the package (and other packages that use it) easier to install and support.
As you may have noticed a large percentage of the GitHub issues are Python
configuration issues (often it's the case that the version the user already
has is somehow mal-configured)
…On Mon, Oct 14, 2019 at 2:05 AM Christophe Dervieux < ***@***.***> wrote:
I see. Thanks for the clarification ! I guess I should always use use_*
to get going. And the message indeed appears only once.
I guess it just feels unexpected when you already have anaconda configured
to get advice to download the little brother miniconda. I would have
considered to be prompted if no Python was found or if on windows not a
python with conda.
But maybe there is a change in reticulate to consider that it should work
better and exclusively with miniconda and it means I should switch from
Anaconda to miniconda ?
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That is completly understandable. This is the approach with TinyTex distribution too, that saves a lot of painful problem with Rmarkdown pdf rendering, regarding LaTex configuration. This is fine by me as when you say no it is not promped again. I'll document internally to our users to use miniconda with reticulate, also specify explicitly the python version. Thanks a lot for your precision. |
I've now made this change: if an Anaconda environment is available, it will be used in preference to Miniconda. |
And what can I do to get that prompt again now that I changed my mind? Thanks! |
The response is stored in a file located at the path referenced by:
If you remove that file, then |
Hello Kevin @kevinushey |
Happens to me just by loading a python script file. |
I'm on a macbook with Big Sur, and I'm brand new to integrating python into my work. For my current project, I'm trying to build a neural network to compare with gbm, rf, glm, and an ensemble... and the python configuration is confusing because the documentation is missing any reference to the workarounds for all of the errors and warnings that RStudio over-engineered into their python-R integration. These warnings and error messages in the R console are very confusing: So far, the tensorflow package installed just fine, but the call
and then the "install_tensorflow()" command prompts you to install a whole new miniconda installation (again, nothing in the webpage for tensorflow install says anything about this). And I just installed the python module to be able to load the tensorflow package, it now seems that running So next, install_tensorflow() seemed to look up a hundred packages that have conflicts with everything in the base 'r-reticulate' environment. Literally everything says there's a conflict. I have no idea what to do about this. I'm not a python expert... I'm just trying to use R to run tensorflow. Here is just one sample of the 3000 lines of illegible output:
And to top it all off, install_tensorflow() seems to have tried to install python 3.7 into my 'r-reticulate' environment, which makes no sense to me at all... and nowhere in the documentation am I reading that R's tensorflow installation requires python 3.7.
So now that this neophyte python user just installed a whole bunch of python crap that was essentially the "wrong version" and named an environment 'r-reticulate' to match RStudio's defaults, there is nowhere in the documentation that teaches you how to "back out" of everything that was just installed, so that I can go back and install anaconda3 under a different python version in the hopes that tensorflow will install again. To say this is incredibly frustrating is an immense understatement. |
* inital skeleton This fully implements the interface for the allowed sceasy conversion routes, but no working backend yet. * better dependencies * Added .shed yaml * Added missing libs, output data * command line implemented * added tests with test-data * fix to .shed.yml * fixed typos, tests now running albeit failing * trying to get reticulate to work 3 tests are failing, and its because pythonhome defaults to system instead of that installed in conda env. One can override this by providing the full path to the conda env, but its not clear if that path is accessible at tool dev level. * Update tools/sceasy/sceasy.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update tools/sceasy/sceasy.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Hack to get CONDA_PREFIX for reticulate to find python. Yeah. * All tests passing * Escaping seems to work now, or it perhaps always did? * Nope, trying with the `use_condaenv' method * TEST * try just the name * make conda visible? * escape * conda is not being found because the python is not being found? see: rstudio/reticulate#607 * missing a colon * set python and condaenv within R * changed toolname and owner * try virtualenv path * Attempt to learn everything we can about the environment we are in... * escape dollar * try again, with command chaining * without find * with find but no exit statement * no command section, just R * again. * found conda prefix, maybe? * normalizePath munges the variable? Let's set the variable directly. * remove junk, enable all tests * hack for biocontainers Please oh please. * removed junk macros * added tool version and version suffix * iuc change * Update tools/sceasy/sceasy.xml Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com> * default to system python if no biocontainer or conda --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com>
It may be by design but I was surprised by this behavior, so I share it
I already have Anaconda installed, and it is found by reticulate, but now I am prompted about miniconda
I would have expected reticulate to find my anaconda installation, and, possibly suggest to switch to miniconda if better. I find it odd to offer to download an other distribution whereas I have one working.
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