Comments (33)
jjtolton
commented on July 1, 2024
As of v1.33 you can do:
(py/initialize! :python-executable "/path/to/executable")and
(py/initialize! :python-executable "/path/to/virtenv/bin/python")I haven't tested this with pipenv yet. Could you try this and let me know if it works? If not I'll change this issue to "make py/initialize! work with pipenv", if that's alright with you :)
Thank you!
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jjtolton
commented on July 1, 2024
I should also point out that py/initialize! needs to be called BEFORE you require [libpython-clj.require :refer [require-python]]. Typically what I do is I will make a separate file like this:
(ns project.python
(:require [libpython-clj.python :as py]))
(py/initialize :python-executable "/path/to/my/env/bin/python")and then in my main namespace
(ns project.core
(:require project.python
[libpython-clj.python :as py :refer [py. py.- py.. py* py**]]
[libpython-clj.require :refer [require-python import-python]]))
(do-fun-stuff!)from libpython-clj.
aaelony
commented on July 1, 2024
Within the pipenv shell it errors out earlier than the py namespace:
$ pipenv shell
Launching subshell in virtual environment…
The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit https://support.apple.com/kb/HT208050.
bash-3.2$ . /Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/activate
(libpython-clj-examples) bash-3.2$ which python
/Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/python
(libpython-clj-examples) bash-3.2$
(libpython-clj-examples) bash-3.2$ clj
Clojure 1.10.1
user=>
user=> (ns gigasquid.seaborn
(:require [libpython-clj.require :refer [require-python]]
[libpython-clj.python :as py :refer [py. py.. py.-]]
[gigasquid.plot :as plot]))
Jan 29, 2020 2:56:47 PM clojure.tools.logging$eval498$fn__501 invoke
INFO: Executing python initialize with options:{:python-executable nil, :program-name nil, :python-home nil, :library-path nil}
Jan 29, 2020 2:56:47 PM clojure.tools.logging$eval498$fn__501 invoke
INFO: Detecting startup-info for Python executable:
Jan 29, 2020 2:56:47 PM clojure.tools.logging$eval498$fn__501 invoke
INFO: Startup info detected: {:python-home "/Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/..", :lib-version "3.8", :libname "python3.8m", :java-library-path-addendum "/Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/../lib"}
Jan 29, 2020 2:56:47 PM clojure.tools.logging$eval498$fn__501 invoke
INFO: Setting java library path: /Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/../lib:/Users/aaelony/Library/Java/Extensions:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java:.
Jan 29, 2020 2:56:47 PM clojure.tools.logging$eval498$fn__501 invoke
INFO: Reference thread starting
Syntax error (ExceptionInfo) compiling at (libpython_clj/metadata.clj:13:1).
Failed to load library
gigasquid.seaborn=>
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aaelony
commented on July 1, 2024
yeah - it fails early:
$ pipenv shell
Launching subshell in virtual environment…
The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit https://support.apple.com/kb/HT208050.
bash-3.2$ . /Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/activate
(libpython-clj-examples) bash-3.2$ which python
/Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/python
(libpython-clj-examples) bash-3.2$ clj
Clojure 1.10.1
user=> (ns project.python
(:require [libpython-clj.python :as py]))
nil
project.python=> (py/initialize! :python-executable
"/Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/python")
Jan 29, 2020 3:02:41 PM clojure.tools.logging$eval492$fn__495 invoke
INFO: Executing python initialize with options:{:python-executable "/Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/python", :program-name nil, :python-home nil, :library-path nil}
Jan 29, 2020 3:02:41 PM clojure.tools.logging$eval492$fn__495 invoke
INFO: Detecting startup-info for Python executable: /Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/python
Jan 29, 2020 3:02:41 PM clojure.tools.logging$eval492$fn__495 invoke
INFO: Startup info detected: {:python-home "/Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/..", :lib-version "3.8", :libname "python3.8m", :java-library-path-addendum "/Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/../lib"}
Jan 29, 2020 3:02:41 PM clojure.tools.logging$eval492$fn__495 invoke
INFO: Setting java library path: /Users/aaelony/.local/share/virtualenvs/libpython-clj-examples-b-Zokxgy/bin/../lib:/Users/aaelony/Library/Java/Extensions:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java:.
Jan 29, 2020 3:02:41 PM clojure.tools.logging$eval492$fn__495 invoke
INFO: Reference thread starting
Execution error (ExceptionInfo) at tech.jna.base/do-load-library (base.clj:158).
Failed to load library
project.python=>
from libpython-clj.
jjtolton
commented on July 1, 2024
Okay, thank you! I'm attempting to reproduce the issue locally.
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aaelony
commented on July 1, 2024
cool, thank-you!!
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jjtolton
commented on July 1, 2024
Okay here's what I setup.
setup
clj -A:new app pipenv.test
cd pipenv.test
python3.7 -m pipenv --python 3.7
python3.7 -m pipenv --venv # to get location of venv
python3.7 -m pipenv install seaborndeps.edn
{:paths ["resources" "src"]
:deps {org.clojure/clojure {:mvn/version "RELEASE"}
cnuernber/libpython-clj {:mvn/version "1.33"}}
:aliases
{:test {:extra-paths ["test"]
:extra-deps {org.clojure/test.check {:mvn/version "RELEASE"}
}}
:runner
{:extra-deps {com.cognitect/test-runner
{:git/url "https://github.com/cognitect-labs/test-runner"
:sha "76568540e7f40268ad2b646110f237a60295fa3c"}}
:main-opts ["-m" "cognitect.test-runner"
"-d" "test"]}}}test.clj
this is where I import Python
Use output of python3.7 -m pipenv --venv as location (plus /bin/python)
(ns pipenv.test
(:require [libpython-clj.python :as py]))
;; replace this with your output from `python3.7 -m pipenv --venv` and then "/bin/python"
(py/initialize! :python-executable "/home/jay/.local/share/virtualenvs/pipenv.test-Rx3tymi4/bin/python")Code
(ns pipenv.core
(:require
pipenv.test
[libpython-clj.python :as py :refer [py. py.- py.. py* py**]]
[libpython-clj.require :refer [require-python import-python]]))
(require-python '[seaborn :as sns])
(require-python '[matplotlib.pyplot :as pyplot])
(comment
(sns/set)
(def dots (sns/load_dataset "dots")))This worked for me. Try following these steps and see if the issue persists.
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jjtolton
commented on July 1, 2024
Oh, I should also mention, don't use pipenv shell. That's not necessary. Might even break something.
Want to emphasize, this is the critical step:
(ns pipenv.test
(:require [libpython-clj.python :as py]))
;; replace this with your output from `python3.7 -m pipenv --venv` and then "/bin/python"
(py/initialize! :python-executable "/home/jay/.local/share/virtualenvs/pipenv.test-Rx3tymi4/bin/python")This needs to be called BEFORE (:require [libpython-clj.require :refer [require-python]]) is imported or it will probably not find the python executable you want
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aaelony
commented on July 1, 2024
getting closer...
I get:
(ns pipenv.test
(:require [libpython-clj.python :as py]
[clojure.java.shell :only [sh]]))
(clojure.java.shell/sh "python3.7" "-m pipenv --venv") => {:exit 1, :out "", :err "/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7: No module named pipenv --venv\n"}
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aaelony
commented on July 1, 2024
doing this first:
pip install seaborn
Creating a virtualenv for this project…
Pipfile: /Users/aaelony/aa/git/github/pipenv.test/Pipfile
Using /usr/local/Cellar/pipenv/2018.11.26_3/libexec/bin/python3.8 (3.8.1) to create virtualenv…
⠼ Creating virtual environment...Already using interpreter /usr/local/Cellar/pipenv/2018.11.26_3/libexec/bin/python3.8
Using real prefix '/usr/local/Cellar/[email protected]/3.8.1/Frameworks/Python.framework/Versions/3.8'
New python executable in /Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y/bin/python3.8
Also creating executable in /Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y/bin/python
Installing setuptools, pip, wheel...
done.
✔ Successfully created virtual environment!
Virtualenv location: /Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y
Creating a Pipfile for this project…
Installing seaborn…
Adding seaborn to Pipfile's [packages]…
✔ Installation Succeeded
Pipfile.lock not found, creating…
Locking [dev-packages] dependencies…
Locking [packages] dependencies…
✔ Success!
Updated Pipfile.lock (fb2b7d)!
Installing dependencies from Pipfile.lock (fb2b7d)…
🐍 ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 11/11 — 00:00:02
To activate this project's virtualenv, run pipenv shell.
Alternatively, run a command inside the virtualenv with pipenv run.
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jjtolton
commented on July 1, 2024
If you're going that route make sure to split on whitespace in clojure.java.shell/sh. Check the example: https://clojuredocs.org/clojure.java.shell/sh#example-542692d6c026201cdc3270ea
You could also do it the stone age way and and just copy/paste from the shell! :P
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jjtolton
commented on July 1, 2024
(clojure.java.shell/sh "python3.7" "-m" "pipenv" "--venv")
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aaelony
commented on July 1, 2024
from the shell I get the same thing:
$ python3.7 -m pipenv --venv
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7: No module named pipenv
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jjtolton
commented on July 1, 2024
Try pipenv --venv instead of python3.7 -m pipenv --venv. Might be different depending on how you installed pipenv. I had to install it with pip since I'm on Ubuntu and don't have brew :O
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aaelony
commented on July 1, 2024
pipenv --venv
works!
or
(ns pipenv.test
(:require [libpython-clj.python :as py]
[clojure.java.shell :only [sh]]
[clojure.string :as str]))
(def venv (-> "pipenv" (clojure.java.shell/sh "--venv") :out str/trim-newline))
venv
Unfortunately though:
(py/initialize! :python-executable venv)
gives
Show: Project-Only All
Hide: Clojure Java REPL Tooling Duplicates (11 frames hidden)
2. Unhandled java.io.IOException
1. Caused by java.io.IOException
error=13, Permission denied
ProcessImpl.java: -2 java.lang.ProcessImpl/forkAndExec
ProcessImpl.java: 340 java.lang.ProcessImpl/<init>
ProcessImpl.java: 271 java.lang.ProcessImpl/start
ProcessBuilder.java: 1107 java.lang.ProcessBuilder/start
Runtime.java: 591 java.lang.Runtime/exec
shell.clj: 113 clojure.java.shell/sh
shell.clj: 79 clojure.java.shell/sh
RestFn.java: 436 clojure.lang.RestFn/invoke
interpreter.clj: 31 libpython-clj.python.interpreter/python-system-data
interpreter.clj: 29 libpython-clj.python.interpreter/python-system-data
interpreter.clj: 75 libpython-clj.python.interpreter/python-system-info
interpreter.clj: 43 libpython-clj.python.interpreter/python-system-info
interpreter.clj: 151 libpython-clj.python.interpreter/detect-startup-info
interpreter.clj: 145 libpython-clj.python.interpreter/detect-startup-info
interpreter.clj: 416 libpython-clj.python.interpreter/initialize!
interpreter.clj: 408 libpython-clj.python.interpreter/initialize!
RestFn.java: 619 clojure.lang.RestFn/invoke
python.clj: 242 libpython-clj.python/initialize!
python.clj: 229 libpython-clj.python/initialize!
RestFn.java: 421 clojure.lang.RestFn/invoke
REPL: 11 pipenv.test/eval34938
core.clj: 3214 clojure.core/eval
core.clj: 3210 clojure.core/eval
main.clj: 437 clojure.main/repl/read-eval-print/fn
main.clj: 458 clojure.main/repl/fn
main.clj: 368 clojure.main/repl
RestFn.java: 1523 clojure.lang.RestFn/invoke
AFn.java: 22 clojure.lang.AFn/run
AFn.java: 22 clojure.lang.AFn/run
Thread.java: 834 java.lang.Thread/run
Unclear how to unlock... perhaps chmod ?
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jjtolton
commented on July 1, 2024
try
(def venv (-> "pipenv" (clojure.java.shell/sh "--venv") :out str/trim-newline (str "/bin/python"))from libpython-clj.
aaelony
commented on July 1, 2024
same error :(
from libpython-clj.
jjtolton
commented on July 1, 2024
what's the value of venv after you do that?
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jjtolton
commented on July 1, 2024
Tell you what, can you head over to https://clojurians.zulipchat.com/#narrow/stream/215609-libpython-clj-dev/topic/help-wanted ? Might be able to help you a little better there.
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aaelony
commented on July 1, 2024
there was a closing ")" missing..
on my system, I need to invoke python3. Unfortunately, /usr/bin/python is python 2.7.
(def venv (-> "pipenv" (clojure.java.shell/sh "--venv") :out str/trim-newline (str "/bin/python3")))
;; venv => "/Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y/bin/python3"
- Unhandled clojure.lang.ExceptionInfo
Failed to load library
{:libname "python3.6m",
:paths
[[:system ["python3.6m"]]
[:java-library-path
["/Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y/bin/../lib/libpython3.6m.dylib"
"/Users/aaelony/Library/Java/Extensions/libpython3.6m.dylib"
"/Library/Java/Extensions/libpython3.6m.dylib"
"/Network/Library/Java/Extensions/libpython3.6m.dylib"
"/System/Library/Java/Extensions/libpython3.6m.dylib"
"/usr/lib/java/libpython3.6m.dylib"
"./libpython3.6m.dylib"]]]}
base.clj: 158 tech.jna.base/do-load-library
base.clj: 123 tech.jna.base/do-load-library
base.clj: 178 tech.jna.base/load-library
base.clj: 174 tech.jna.base/load-library
jna.clj: 87 tech.jna/load-library
jna.clj: 85 tech.jna/load-library
interpreter.clj: 404 libpython-clj.python.interpreter/setup-direct-mapping!
interpreter.clj: 402 libpython-clj.python.interpreter/setup-direct-mapping!
interpreter.clj: 441 libpython-clj.python.interpreter/initialize!
interpreter.clj: 408 libpython-clj.python.interpreter/initialize!
RestFn.java: 619 clojure.lang.RestFn/invoke
python.clj: 242 libpython-clj.python/initialize!
python.clj: 229 libpython-clj.python/initialize!
RestFn.java: 421 clojure.lang.RestFn/invoke
REPL: 21 pipenv.test/eval34964
core.clj: 3214 clojure.core/eval
core.clj: 3210 clojure.core/eval
main.clj: 437 clojure.main/repl/read-eval-print/fn
main.clj: 458 clojure.main/repl/fn
main.clj: 368 clojure.main/repl
RestFn.java: 1523 clojure.lang.RestFn/invoke
AFn.java: 22 clojure.lang.AFn/run
AFn.java: 22 clojure.lang.AFn/run
Thread.java: 834 java.lang.Thread/run
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jjtolton
commented on July 1, 2024
so from a fresh REPL
user=> (require '[libpython-clj.python :as py])
nil
user=> (py/initialize! :python-executable "/Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y/bin/python3")Give that a shot and see if it works
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cnuernber
commented on July 1, 2024
We need the shared library produced when you install the virtual env.
Really what we need is an environments.md file under docs that describes that issue and this one and the fix (if Stuart's fix works for you).
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aaelony
commented on July 1, 2024
Not working just yet... getting Failed to load library as error.
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cnuernber
commented on July 1, 2024
Did you try with the suggested env variable when installing the env?
env PYTHON_CONFIGURE_OPTS="--enable-framework" pyenv install 3.6.9
Specifically, where is the python3.6m shared library on your system if you search?
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aaelony
commented on July 1, 2024
I think that is the issue. I need to set the env variable correctly. My system is literally litered with such libs.
/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/libpython3.7m.dylib
/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/config-3.7m-darwin/libpython3.7m.dylib
/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/libpython3.7m.dylib
/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/python3.7/config-3.7m-darwin/libpython3.7m.dylib
/Library/Frameworks/Python.framework/Versions/3.7/lib/libpython3.7m.dylib
/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/config-3.7m-darwin/libpython3.7m.dylib
/System/Volumes/Data/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/libpython3.7m.dylib
/System/Volumes/Data/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/config-3.7m-darwin/libpython3.7m.dylib
/System/Volumes/Data/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/libpython3.7m.dylib
/System/Volumes/Data/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/python3.7/config-3.7m-darwin/libpython3.7m.dylib
/System/Volumes/Data/Library/Frameworks/Python.framework/Versions/3.7/lib/libpython3.7m.dylib
/System/Volumes/Data/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/config-3.7m-darwin/libpython3.7m.dylib
/System/Volumes/Data/Users/aaelony/python/miniconda3/pkgs/python-3.7.4-h359304d_1/lib/libpython3.7m.dylib
/System/Volumes/Data/Users/aaelony/python/miniconda3/lib/libpython3.7m.dylib
/Users/aaelony/python/miniconda3/pkgs/python-3.7.4-h359304d_1/lib/libpython3.7m.dylib
/Users/aaelony/python/miniconda3/lib/libpython3.7m.dylib
Unfamiliar with a good way to housekeep, hence the need for sandboxing.
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cnuernber
commented on July 1, 2024
This is why I recommend using docker. We have a clear example of how to use docker including mounting your local project here. Essentially docker is the most sandboxed you can get :-).
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aaelony
commented on July 1, 2024
Totally. I'll look into the facial-rec example you provided.
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jjtolton
commented on July 1, 2024
I'm trying to determine if py/initialize! is what is crashing or if the require-python is causing the issue. I'm not sure where the Failed to load library message is coming from -- I don't think that originates directly from libpython-clj.
Also I wonder if this is a Mac specific issue or there's just some local environment stuff going on. I managed to get pipenv working on Ubuntu. If I get some time I'll test on a Mac and see if it comes up there.
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aaelony
commented on July 1, 2024
Here is the current state of progress:
$ clj
Clojure 1.10.1
(ns pipenv.test
(:require [libpython-clj.python :as py]
[clojure.java.shell :only [sh]]
[clojure.string :as str]))
nil
pipenv.test=>
pipenv.test=> (def venv (-> "pipenv" (clojure.java.shell/sh "--venv") :out str/trim-newline (str "/bin/python3")))
#'pipenv.test/venv
pipenv.test=>
pipenv.test=> venv
"/Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y/bin/python3"
pipenv.test=> (py/initialize! :python-executable venv)
Jan 30, 2020 11:03:15 AM clojure.tools.logging$eval492$fn__495 invoke
INFO: Executing python initialize with options:{:python-executable "/Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y/bin/python3", :program-name nil, :python-home nil, :library-path nil}
Jan 30, 2020 11:03:15 AM clojure.tools.logging$eval492$fn__495 invoke
INFO: Detecting startup-info for Python executable: /Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y/bin/python3
Jan 30, 2020 11:03:16 AM clojure.tools.logging$eval492$fn__495 invoke
INFO: Startup info detected: {:python-home "/Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y/bin/..", :lib-version "3.8", :libname "python3.8m", :java-library-path-addendum "/Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y/bin/../lib"}
Jan 30, 2020 11:03:16 AM clojure.tools.logging$eval492$fn__495 invoke
INFO: Setting java library path: /Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y/bin/../lib:/Users/aaelony/Library/Java/Extensions:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java:.
Jan 30, 2020 11:03:16 AM clojure.tools.logging$eval492$fn__495 invoke
INFO: Reference thread starting
Execution error (ExceptionInfo) at tech.jna.base/do-load-library (base.clj:158).
Failed to load library
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jjtolton
commented on July 1, 2024
I haven't tested on Python 3.8 yet. I'll see if I can give that a shot.
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cnuernber
commented on July 1, 2024
@aaelony - does libpython3.8m.dylib exist at :java-library-path-addendum "/Users/aaelony/.local/share/virtualenvs/pipenv.test-QmYINU7y/bin/../lib"?
If not, then my question is was the env installed with
env PYTHON_CONFIGURE_OPTS="--enable-framework" pyenv install 3.8The system thinks that the python shared library is installed at the above location.
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gigasquid
commented on July 1, 2024
That was my thought too @aaelony - it kinda looks like this issue #61
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jjtolton
commented on July 1, 2024
@cnuernber recommend closing. Tested that pipenv works for Ubuntu (see details above). If it doesn't work for Mac that would be a separate issue. @aaelony if you're continuing to experience problems please visit out help-wanted topic and we'll continue to assist until you get it!
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- Newbie: Lein Clojure Windows Anaconda VSCode Cava REPL Returns (NoClassDefFoundError) HOT 5
- Create Python Module then Import Module and Call Function Inside Clojure? HOT 4
- Fix ubuntu version in dockerfiles HOT 6
- Consider releasing returned values from instance fns
- JDK-20 support HOT 3
- builtins/eval throws 'frame does not exist' HOT 2
- Unable to require libraries from within docker using conda HOT 6
- Failed to find a valid python library on MS-Windows with the official python distributions
- Extend CI coverage to all the mainstream architectures
- require-python missing functions with annotation HOT 3
- Make polyglot development easier by allow require-python to be path-informed HOT 1
- Data transformation pipelines? HOT 1
- NSWindow main thread error when trying to setup Gymnasium (openapi gym) HOT 5
- JVM crashes when requiring `libpython-clj2.require` on 64bit Raspberry Pi 4 HOT 1
- error of unhashable type HOT 15
- Ways to reduce probability of memory leaks? HOT 2
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from libpython-clj.