Not able to install CyLP on windows - python

I am trying to install CyLP. I downloaded the cbc package.Then it says to run the following commands:
$ ./configure
$ make
$ make install
But these commands do not run in command prompt.So, how do I run them.Also, I tried the following command for pip install:
pip install -i https://pypi.anaconda.org/pypi/simple cylp
But, it gave me the error that cbc files were not found found.So , how do I install CyLP in windows.

I have recently worked with cylp package but on linux. So I am not sure that it is available for windows but there can be a quick fix to this problem on windows.
For working of make and make install on windowsHere are a few ports of GNU tools to Windows:
GnuWin32 - http://gnuwin32.sourceforge.net/summary.html
Gnu Tools for NT - http://www.devhood.com/Tools/tool_details.aspx?tool_id=3
GNU Utilities for Win32 - http://unxutils.sourceforge.net/
For working of ./configure on windows - I would install the MINGW/MSYS development tools and see if the configure script is happy in that environment.
EDIT
Okay So I finally came up with the solution on how to install CYLP on windows. I would recommend you to:
Try the following
Create a new environment for 32bit Python 2.7:
set CONDA_FORCE_32BIT=1
conda create -n py27_32 python=2.7
Activate it:
set CONDA_FORCE_32BIT=1
activate py27_32
install cylp:
conda install scipy
pip install cylp

Related

How can I run pyqt5 on my Mac with M1chip (ppc64el architecture)?

Now. When I run it. The error comes
ImportError:
dlopen(/Users/v/Library/Python/3.8/lib/python/site-packages/PyQt5/QtWidgets.abi3.so,
2): no suitable image found. Did find:
/Users/v/Library/Python/3.8/lib/python/site-packages/PyQt5/QtWidgets.abi3.so:
mach-o, but wrong architecture
/Users/v/Library/Python/3.8/lib/python/site-packages/PyQt5/QtWidgets.abi3.so:
mach-o, but wrong architecture
After hours of trial and error, I was finally able to solve this. My successful configuration is:
Open terminal with Rosetta 2 (https://dev.to/courier/tips-and-tricks-to-setup-your-apple-m1-for-development-547g)
Use non-homebrew python (mine was in /usr/bin/python3) to create virtual environment
/usr/bin/python3 -m venv env
source env/bin/activate
Upgrade pip
pip install --upgrade pip
Install PyQt5
pip install PyQt5
I needed PyQt5 as a dependency for a Python library and this worked for me. See original post here.
brew install pyqt5
echo 'export PATH="/opt/homebrew/opt/qt#5/bin:$PATH"' >> ~/.zshrc
echo 'export PATH="/opt/homebrew/opt/pyqt#5/5.15.4_1/bin:$PATH"' >> ~/.zshrc
source ~/.zshrc
What I ended up doing specifically for pyqt5 was:
brew install pyqt#5
I think for versions 4 and 6 this may work as well. When I went simply brew install pyqt that didn't work unfortunately.
note this is M1 Macbook only
One other thing to try as things settle down with M1s is to try pip3 install pyqt5 in a terminal launched in Rosetta mode (left click -> Get Info -> Open in Rosetta)
Edit (Nov 2022)
It seems that if you don't specifically need pyqt5, pyqt6 is now easily installable via pip on M1/M2 Macs.
python -m pip install pyqt6
I was hoping to install pyqt5 on my M1 mac without Rosetta. I was using it as a dependency of another project that I wanted to install in a venv which requires pyqt5 and was not installable via pipx (urh).
Unfortunately, there currently are no compatible wheels (curl --silent "https://pypi.org/pypi/PyQt5/json" | grep -i arm64), and attempting to install on 3.10 fails with AttributeError: module 'sipbuild.api' has no attribute 'prepare_metadata_for_build_wheel'
Thankfully, the homebrew installation of pyqt5 is compiled for arm64 and works well.
My steps were:
$ # Install pyqt5 via homebrew
$ brew install pyqt#5
$ # Note that it's installed in python3.9, not 3.10
$ brew cat pyqt#5 | grep 'depends_on.*python'
depends_on "python#3.9"
$ # Make a python3.9 virtualenv with access to the system's site-packages
$ /opt/homebrew/bin/python3.9 -m venv --system-site-packages .venv
$ source .venv/bin/activate
At this point I was able to install urh into the virtualenv, using the arm64-compiled pyqt5 from hombrew, without neededing Rosetta (and without needing to further "pollute" my system site-packages), and it runs as expected (since the question was about running).
Try installing the pyqt under the ARM architecture as below
arch -arm64 brew install pyqt
In my case it's work: arch -x86_64 brew install pyqt
And all required pyqt start from arch -x86_64 or start from rosetta (through emulator).
You can use it from homebrew, this is the only way I found it working on Mac M1.
First:
brew install pyqt#5
Then:
brew --cellar
brew link --overwrite python
Then you must create/add an alias for python and put it in your .zprofile (Located in Users/username folder, if you press Shift+command+.
This must point to your homebrew python installation location.
alias python ='opt/homebrew/bin/python3'
That way it will link python with your homebrew python and you can run python test.py from terminal (Where your python files are located).
No matter how I tried with pip install, it just shown error and did not work.
I wanted to run PyQt5 under virtual environment with Python3.6.
The following procedures worked for me.
My settings are MBA M1 2020, macOS 11.3.1, and
pyenv versions
> system
> * 3.6.15
pip -V
> pip 21.3.1 from /Users/username/.pyenv/versions/3.6.15/lib/python3.6/site-packages/pip (python 3.6)
Then simply run:
pip install pyqt5-sip
pip install pyqt5
on the terminal (default one, not the one with Rosetta 2).
I had to install PyQt5==5.15.6on my MacM1 into an existing virtual environment.
It did not work using all the methods described here.
So, what I did is :
Open the terminal in rosetta mode
Navigate to my project and activate the virtual environment source venv/bin/activate
Install the package : pip install PyQt5==5.15.6
Open a regular terminal into my project and make sure everything was installed as per the requirements.txt : pip install -r requirements.txt
Everything is running smoothly, now.
If anyone is still having the same problem with installation of PyQT5, I would suggest you to rather lock your focus on PySide6. It is 99% similar to PyQT5 and works well with MacBook m1.
I've been digging the Internet for hours hoping to find the solution but it appears that PyQT5 and PyQT5-tools modules are somewhat broken on MacBook M1 when it comes to downloading them.
I was struggling with installing PyQt5 on M1 mac with MacOS 12.6 (Monterey) inside a virtual environment (using python 3.9). The final solution that worked for me was to use conda for creating and activating the virtual environment.
conda create --name venv python=3.9 conda activate venv
And then simply using conda to install PyQt5 as part of the pyqt package.
conda install pyqt
PyQt6 is out now and supports apple silicon:
https://stackoverflow.com/a/75224682/19486832
No conda support, but pip install is working fine:
python -m pip install PyQt6

Installing bioinformatics packages like bowtie2 in windows through WSL

I'm trying to develop a GUI in python for analyze tRNA-Seq data which could be run in Linux and Windows. For this it is needed run some programs like: bowtie2, samtools or bedtools, which can be downloaded by anaconda easily on Linux but is a headache on Windows. This programs can't be downloaded on Windows so I had to install Windows Subsystem for Linux (WSL) and tried to downloaded by this way.
I have developed the following python script (anaconda_setup.py) for doing this:
import os
#Download the file for Linux, altough this script will run only on Windows Subsystem for Linux
os.system('curl -O https://repo.anaconda.com/archive/Anaconda3-2020.07-Linux-x86_64.sh')
#Checking the integrity of the file
os.system('sha256sum Anaconda3-2020.07-Linux-x86_64.sh')
#Running the .sh script
os.system('bash Anaconda3-2020.07-Linux-x86_64.sh')
#Compiling from source
os.system('source ~/.bashrc')
os.system('Anaconda3-2020.07-Linux-x86_64.sh')
#Using conda to install bowtie2, samtools and bedtools
os.system('conda install -c bioconda bowtie2')
os.system('conda install -c bioconda samtools')
os.system('conda install -c bioconda bedtools')
And then I use the following code in the main script for call the other script:
import os
...
os.system("wsl python3 anaconda_setup.py")
With this anaconda is installed correctly, but I'm not sure if it is installed on windows or in WSL. But I obtained the next error:
sh: 1: source: not found
sh: 1: conda: not found
sh: 1: conda: not found
sh: 1: conda: not found
On the other hand I have entered to WSL from CMD and I can run conda.exe and conda manually, but I can't do it in an automatically way. Moreover from CMD I can't run: "wsl conda" (error: /bin/bash: conda: command not found) but I can run wsl conda.exe without anyproblem.
Any idea what I'm doing wrong or how can I fix this?
Thank you very much.
Use Linux installers for anaconda to install anaconda for wsl2
wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.9.2-Linux-x86_64.sh
check if conda command runs, if not, the path must be exported in .bashrc file
export PATH=/home/user/anaconda3/bin:$PATH
run conda again, it will work now. You can install your required software using conda in wsl2.
Hope this helps you out. For more info visit this
post
Here are the steps you can follow.
you have to have Ubuntu terminal installed. If not download it from Microsoft Store.
After installing Ubuntu install wget using command sudo apt install wget
Install miniconda because miniconda is lighter version of anaconda and will save up a lot of space.
Download miniconda installer.
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Install miniconda bash Miniconda3-latest-Linux-x86_64.sh
export PATH export PATH=~/miniconda3/bin:$PATH
Install bowtie2 using bioconda channel conda install -c bioconda bowtie2

Pipenv: Command Not Found

I'm attempting to use pipenv. I ran the command pip install pipenv, which ran successfully:
...
Successfully built pipenv pathlib shutilwhich pythonz-bd virtualenv-clone
Installing collected packages: virtualenv, pathlib, shutilwhich, backports.shutil-get-terminal-size, pythonz-bd, virtualenv-clone, pew, first, six, click, pip-tools, certifi, chardet, idna, urllib3, requests, pipenv
...
However, when I run the command pipenv install in a fresh root project directory I receive the following message: -bash: pipenv: command not found. I suspect that I might need to modify my .bashrc, but I'm unclear about what to add to the file or if modification is even necessary.
This fixed it for me:
sudo -H pip install -U pipenv
That happens because you are not installing it globally (system wide). For it to be available in your path you need to install it using sudo, like this:
$ sudo pip install pipenv
If you've done a user installation, you'll need to add the right folder to your PATH variable.
PYTHON_BIN_PATH="$(python3 -m site --user-base)/bin"
PATH="$PATH:$PYTHON_BIN_PATH"
See pipenv's installation instructions
I tried this:
python -m pipenv # for python2
python3 -m pipenv # for python3
Why this works: In Bash and other Unix-like shell environments, the -m option is used to specify a module to be run as a script.
When you run a Python script using the python -m command, you are telling the Python interpreter to execute the script as if it were a top-level module, rather than as a script file. The python -m pipenv command tells the Python interpreter to run the pipenv module as a script. The pipenv module must be importable from the current working directory or from one of the directories in the PYTHONPATH environment variable.
I have same problem with pipenv on Mac OS X 10.13 High Seirra, another Mac works just fine. I use Heroku to deploy my Django servers, some in 2.7 and some in 3.6. So, I need both 2.7 and 3.6. When HomeBrew install Python, it keeps python points to original 2.7, and python3 points to 3.6.
The problem might due to $ pip install pipenv. I checked /usr/local/bin and pipenv isn't there. So, I tried a full uninstall:
$ pip uninstall pipenv
Cannot uninstall requirement pipenv, not installed
You are using pip version 9.0.1, however version 10.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
$ pip3 uninstall pipenv
Skipping pipenv as it is not installed.
Then reinstall and works now:
$ pip3 install pipenv
Collecting pipenv
Where Python store packages
Before jumping into the command that will install pipenv, it is worth understanding where pip installs Python packages.
Global site-packages is where Python installs packages that will be available to all users and all Python applications on the system. You can check the global site package with the command
python -m site
For example, on Linux with Python 3.7 the path is usually
/usr/lib/python3.7/dist-packages/setuptools
User site-packages is where Python installs packages available only for you. But the packages will still be visible to all Python projects that you create. You can get the path with
python -m site --user-base
On Linux with Python 3.7 the path is usually
~/.local/lib/python3.7/site-packages
Using Python 3.x
On most Linux and other Unices, usually Python 2 and Python 3 is installed side-by-side. The default Python 3 executable is almost always python3. pip may be available as either of the following, depending on your Linux distribution
pip3
python3-pip
python36-pip
python3.6-pip
Linux
Avoid using pip with sudo! Yes, it's the most convenient way to install Python packages and the executable is available at /usr/local/bin/pipenv, but it also mean that specific package is always visible for all users, and all Python projects that you create. Instead, use per-user site packages instead with --user
pip3 install --user pipenv
pipenv is available at
~/.local/bin/pipenv
macOS
On macOS, Homebrew is the recommended way to install Python. You can easily upgrade Python, install multiple versions of Python and switch between versions using Homebrew.
If you are using Homebrew'ed Python, pip install --user is disabled. The global site-package is located at
/usr/local/lib/python3.y/site-packages
and you can safely install Python packages here. Python 3.y also searches for modules in:
/Library/Python/3.y/site-packages
~/Library/Python/3.y/lib/python/site-packages
Windows
For legacy reasons, Python is installed in C:\Python37. The Python executable is usually named py.exe, and you can run pip with py -m pip.
Global site packages is installed in
C:\Python37\lib\site-packages
Since you don't usually share your Windows devices, it is also OK to install a package globally
py -m pip install pipenv
pipenv is now available at
C:\Python37\Scripts\pipenv.exe
I don't recommend install Python packages in Windows with --user, because the default user site-package directory is in your Windows roaming profile
C:\Users\user\AppData\Roaming\Python\Python37\site-packages
The roaming profile is used in Terminal Services (Remote Desktop, Citrix, etc) and when you log on / off in a corporate environment. Slow login, logoff and reboot in Windows can be caused by a large roaming profile.
OSX GUYS, OVER HERE!!!
As #charlax answered (for me the best one), you can use a more dynamic command to set PATH, buuut for mac users this could not work, sometimes your USER_BASE path got from site is wrong, so you need to find out where your python installation is.
$ which python3
/usr/local/bin/python3.6
you'll get a symlink, then you need to find the source's symlink.
$ ls -la /usr/local/bin/python3.6
lrwxr-xr-x 1 root wheel 71 Mar 14 17:56 /usr/local/bin/python3.6 -> ../../../Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6
(this ../../../ means root)
So you found the python path (/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6), then you just need to put in you ~/.bashrc as follows:
export PATH="$PATH:/Library/Frameworks/Python.framework/Versions/3.6/bin"
Installing pipenv globally can have an adverse effect by overwriting the global/system-managed pip installation, thus resulting in import errors when trying to run pip.
You can install pipenv at the user level:
pip install --user pipenv
This should install pipenv at a user-level in /home/username/.local so that it does not conflict with the global version of pip. In my case, that still did not work after running the '--user' switch, so I ran the longer 'fix what I screwed up' command once to restore the system managed environment:
sudo python3 -m pip uninstall pip && sudo apt install python3-pip --reinstall
^ found here: Error after upgrading pip: cannot import name 'main'
and then did the following:
mkdir /home/username/.local ... if it doesn't already exist
export PYTHONUSERBASE=/home/username/.local
Make sure the export took effect (bit me once during this process):
echo $PYTHONUSERBASE
Then, I ran the pip install --user pipenv and all was well. I could then run pipenv from the CLI and it did not overwrite the global/system-managed pip module. Of course, this is specific to the user so you want to make sure you install pipenv this way while working as the user you wish to use pipenv.
References:
https://pipenv.readthedocs.io/en/latest/diagnose/#no-module-named-module-name https://pipenv.readthedocs.io/en/latest/install/#pragmatic-installation-of-pipenv https://pip.pypa.io/en/stable/user_guide/#user-installs
I don't know what happened, but the following did the work (under mac os catalina)
$ brew install pipenv
$ brew update pipenv
after doing this i am able to use
$ pipenv install [package_name]
OS : Linux
Pip version : pip3
sudo -H pip3 install -U pipenv
OS : Windows
Pip version : any one
sudo -H pip install -U pipenv
For thse who installed it using sudo pip3 install pipenv, you need to use python3 -m pipenv shell or python3.9 -m pipenv shell
I'm using zsh on my Mac, what worked for me is at first install pipenv
pip3 install --user pipenv
Then I changed the PATH in the ~/.zshrc
vi ~/.zshrc
In the editor press i to insert your text:
export PATH="/Users/yourUser/Library/Python/3.9/bin:$PATH"
Press esc and then write :wq!
Close the terminal and re-open it.
And finally write pipenv
This way worked for me using macOS BigSur 11.1
On Mac you may have to do:
pip3 install pipenv
Then, cd into your root directory to locate the .zshrc file.
Then add this to path
export PATH=/Library/Frameworks/Python.framework/Versions/3.9/bin:$PATH
Note: 3.9 is the version of Python running on your system.
Note: You can access the .zshrc by using cmd + shift + .
in your root directory... the file is hidden by default
Save and restart your terminal
Fixed this easily by installing pipenv with my central package manager (apt)
sudo apt install pipenv
You could easily install pipenv using your package manager (apt, yum, brew) and it adds it directly to your $PATH variables.
More to mention is it works on zsh. I use zsh on Ubuntu and tried adding pipenv to $PATH and other solutions but didn't work till I used apt to install it.
HOW TO MAKE PIPENV A BASIC COMMAND
Pipenv with Python3 needs to be run as "$ python -m pipenv [command]" or "$ python3 -m pipenv [command]"; the "python" command at the beginning varies based on how you activate Python in your shell. To fix and set to "$ pipenv [command]": [example in Git Bash]
$ cd ~
$ code .bash_profile
The first line is necessary as it allows you to access the .bash_profile file. The second line opens .bash_profile in VSCode, so insert your default code editor's command.
At this point you'll want to (in .bash_profile) edit the file, adding this line of code:
alias pipenv='python -m pipenv'
Then save the file and into Git Bash, enter:
$ source .bash_profile
You can then use pipenv as a command anywhere, for example:
$ pipenv shell
Will work.
This method of usage will work for creating commands in Git Bash. For example:
alias python='winpty python.exe'
entered into the .bash_profile and:
$ source .bash_profile
will allow Python to be run as "python".
You're welcome.
On Mac OS X Catalina it appears to follow the Linux path. Using any of:
pip install pipenv
pip3 install pipenv
sudo pip install pipenv
sudo pip3 install pipenv
Essentially installs pipenv here:
/Users/mike/Library/Python/3.7/lib/python/site-packages/pipenv
But its not the executable and so is never found. The only thing that worked for me was
pip install --user pipenv
This seems to result in an __init__.py file in the above directory that has contents to correctly expose the pipenv command.
and everything started working, when all other posted and commented suggestions on this question failed.
The pipenv package certainly seems quite picky.
If you are on MAC
sudo -H pip3 install pipenv
For window users this may be due to conflicting installation with virtualenv. For me it worked when I uninstalled virtualenv and pipenv first, and then install only pipenv.
pip uninstall virtualenv
pip uninstall pipenv
pip install pipenv
Now pipenv install xxx worked for me
After installing pipenv (sudo pip install pipenv), I kept getting the "Command Not Found" error when attempting to run the pipenv shell command.
I finally fixed it with the following code:
pip3 install pipenv
pipenv shell
Here is how I successfully resolved "Pipenv: Command Not Found" on my Mac OSX
You should change the ownership of these directories to your user.
sudo chown -R $(whoami) /usr/local/share
make sure that your user has write permission.
chmod u+w /usr/local/share
Then Consider installing with Homebrew:
brew update
brew install pyenv
This simply solved it for me if you are on windows.
pip install pipenv
Second, replace your <username> in the following paths and add them to the PATH environment variable:
c:\Users\<username>\AppData\Roaming\Python\Python38\Site-Packages
C:\Users\<username>\AppData\Roaming\Python\Python38\Scripts
You need to close the Command Prompt and reopen it.
Third, type the following command to check if the pipenv installed correctly:
pipenv -h
I hope this helps you too!
In this case you just need to add the binary path to your bash. In case you're using ZSH for example you need to edit the.zshrc file as an admind and then add the code mentioned by #charlax on the comments above:
PYTHON_BIN_PATH="$(python3 -m site --user-base)/bin"
PATH="$PATH:$PYTHON_BIN_PATH"
You might consider installing pipenv via pipsi.
curl https://raw.githubusercontent.com/mitsuhiko/pipsi/master/get -pipsi.py | python3
pipsi install pew
pipsi install pipenv
Unfortunately there are some issues with macOS + python3 at the time of writing, see 1, 2. In my case I had to change the bashprompt to #!/Users/einselbst/.local/venvs/pipsi/bin/python
In some cases of old pip version:
sudo easy_install pip
sudo pip install pipenv
First check if pipenv is installed:
pipenv --version
If no version is available on your system, then run the following command to install pipenv
sudo aptitude install pipenv
first install pip using following command
pip3 install pipenv
Now check whether pipenv is showing by using following command
pipenv --version if you see like command not found: pipenv use following commands
Now we have to set the path for pipenv, to do that first we have to find the user base binary directory,
On linux and Mac we can do it as following
python3 -m site --user-base
this command will display something like this
/some_directory/Python/3.9
use the path displayed in your terminal and append /bin at the end, now your path looks like this
/some_directory/Python/3.9/bin
now you have to set the path, if you are using zsh (z shell) type nano ~/.zshrc in the terminal or if you are using code editor like VSCode and path is set for VScode type code ~/.zshrc
if you are using bash use nano ~/.bashrc or code ~/.bashrc
in the file at last add following line
export PATH="$PATH:/somedirectory/Python/3.9/bin"
save the file and exit the terminal
now open new terminal and type pipenv --version you should see something like pipenv, version 2022.10.25
on Windows we can do as following
python -m site --user-site
you should see something like
C:\Users\Username\AppData\Roaming\Python36\site-packages`
now replace site-packages with Scripts.
this could return
C:\Users\Username\AppData\Roaming\Python36\Scripts
You can set your user PATH permanently in the Control Panel. You may need to log out for the PATH changes to take effect.
It's probably installed in your user path.
for instance, if your user(username) is tom check this path
/home/tom/.local/bin/pipenv
if pipenv exists in the path you can move or copy it to the general user path, so you can execute pipenv from all terminal sessions.
cp /home/tom/.local/bin/pipenv /usr/bin/
then you should be able to run pipenv
For me, what worked on Windows was running Command Prompt as administrator and then installing pipenv globally: python -m pip install pipenv.

pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available

I am using Python 3.6. When I try to install "modules" using pip3, I face this issue:
pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available
For Windows 10
if you want use pip in normal cmd, not only in Anaconda prompt. you need add 3 environment paths.
like the followings:
D:\Anaconda3
D:\Anaconda3\Scripts
D:\Anaconda3\Library\bin
most people only add D:\Anaconda3\Scripts
MAC OS
I had the same problem on Mac OS(Mojave) and solved the problem as mentioned on this link - Openssl issue.
If you do not have Homebrew or don't know what is Homebrew:
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
Or if you already have Homebrew installed:
brew update && brew upgrade
brew uninstall --ignore-dependencies openssl; brew install https://github.com/tebelorg/Tump/releases/download/v1.0.0/openssl.rb
Update:
Keep in mind, that I had to use --ignore-dependencies flag, because other packages installed that depend on OpenSSL.
Additional if the problem is caused after using pyenv, you can fix it by using:
brew reinstall python
For Debian users, the following may be of use:
sudo apt install libssl-dev libncurses5-dev libsqlite3-dev libreadline-dev libtk8.6 libgdm-dev libdb4o-cil-dev libpcap-dev
Then cd to the folder with the Python 3.X library source code and run:
./configure
make
make install
I'm using Windows 10 and installed Miniconda 3 with Python 3.7.
I solved this error by following this https://github.com/conda/conda/issues/8273
Specifically, I copied the following files from C:\Users\MyUser\Miniconda3\Library\bin to C:\Users\MyUser\Miniconda3\DLLs:
libcrypto-1_1-x64.dll
libcrypto-1_1-x64.pdb
libssl-1_1-x64.dll
libssl-1_1-x64.pdb
For centos 7:
Install openssl:
sudo yum install openssl-devel
now goto python directory were we extracted the python tar,
run below commands
sudo ./configure
sudo make
sudo make install
This will fix the problem in centos...
For future Oracle Linux users trying to solve this, below is what worked for me.
First install missing libs:
yum install zlib-devel bzip2-devel openssl-devel ncurses-devel sqlite-devel
readline-devel tk-devel gdbm-devel db4-devel libpcap-devel xz-devel
Then cd to your Python3.X library and run:
make
make install
macOS, pyenv
In case of your python being an pyenv installed one, where pyenv is installed with homebrew on macOS, there might me a newer version available which fixes this:
$ brew update && brew upgrade pyenv
Then reinstalling the python version:
$ pyenv install 3.7.2
pyenv: /Users/luckydonald/.pyenv/versions/3.7.2 already exists
continue with installation? (y/N)
Note, it is a bit dirty to overwrite the existing python install like that, but in my case it did work out. Probably cleaner to delete it and then recreate it properly.
For Windows 10,windows 7
If pip install is not working on CMD prompt, run it using Anaconda prompt - it works.
https://github.com/pypa/virtualenv/issues/1139
Worked for me.
sudo apt-get install libssl-dev
Use this to enable ssl for pip.
Let me know if someone encounters issues.
Encountered this issue while installing python 3.8 from source on ubuntu. The steps needed to install it successfully alongside the default python 3.7 are summarised below :
sudo apt -y install libssl-dev zlib1g-dev build-essential
wget https://www.python.org/ftp/python/3.8.0/Python-3.8.0.tgz
tar -xf Python-3.8.0.tgz
cd Python-3.8.0/
./configure --enable-optimizations
make
sudo make altinstall
The install instruction for zlib1g-dev and build-essential is redundant, as ubuntu desktop already has these, but was necessary for some of Amazon's EC2 instances. python 3.8.0 is the current release just now, but should be replaced with the latest available.
These instructions are best for keeping python 3.7 as the default for python3, and running python 3.8 in a virtual environment.
Similar to the above solution reinstall the python version with pyenv.
Somehow, I upgraded my openssl which broke the pyenv version python.
pyenv install 3.6.8
python-build: use openssl#1.1 from homebrew
python-build: use readline from homebrew
...
The first line says it relies on the homebrew openssl.
In my case, I reinstalled Python. It solved the problem.
brew reinstall python
For OpenSUSE in the same manner, but a few changes of listed above packages:
zypper install zlib-devel libopenssl-devel ncurses-devel sqlite3-devel readline-devel tk-devel gdbm-devel libpcap-devel xz-devel
Then cd to Python sources dir and
make
make install
or
make
make altinstall
And perhaps
ln -s /usr/local/lib64/python3.6/lib-dynload/ /usr/local/lib/python3.6/lib-dynload
should be executed for OpenSUSE users. See Python 3.7 install not working on openSUSE Leap 42.3
Just try installing through Anaconda prompt
I ran into this issue with Visual Studio Code installing pylint from the VS Code prompt.
I was able to overcome the issue by opening the Anaconda installation directory and running
pip install pylint
Then VS Code was happy, but that did not fix the issue as running
& C:/Users/happy/Anaconda3/python.exe -m pip install -U pylint
pretty much gave the same error so it seems that VS Code is unable to access the python modules.
Note that VS Code picks up the first python env it see when installed, the bottom left of the screen indicates which env is being used. Clicking on that area allows to set the environment. So even if you ran the pip install for an environment VS Code could be looking at a different one.
Best approach was to make sure that VS code had the correct python environment selected and that same environment is in the system PATH (under System Properties --> Advanced --> Environmental Variables)
Under the Path Variable, Edit and browse to the specific Anaconda directory that you want VSCode to use and add to PATH, I needed to Add the following:
C:\Users\happy\Anaconda3\
C:\Users\happy\Anaconda3\Scripts\
C:\Users\happy\Anaconda3\Library\bin\
C:\Users\happy\Anaconda3\Library\mingw-w64\bin\
Your Anaconda installation directory may differ.
One note is that Windows does not have the PATH variable take effect until you restart the terminal. In this case close and re-op VS code. If using a Terminal or PS Shell then close and reopen and check Path to make sure it is included.
The problem probably comes from your installed openssl package version. That was the case for me and I fixed this issue just upgrading it. I'm on Mac OS, using brew :
brew upgrade openssl
If you installed python with brew, this should directly fix the issue with it, as python is dependent on openssl
Newest Python 3.8.4 or higher should able to support https protocol out of box. If you still have old python installation on your pc - either download & install python3 manually, or using Chocolatey:
If you don't have Chocolatey, install it - from here: https://chocolatey.org/docs/installation
You can just copy paste one command line liner and execute it from command prompt with elevated priviledges.
choco install python3
if you don't have python3 installed, or you you have it installed - then:
choco upgrade python3
Notice also that you can use also anaconda distribution, as it has built-in python with https support, but this rather ancient instructions, no need to follow them anymore.
Install anaconda, using command line:
choco install anaconda3
Set environment variables:
set PATH=C:\tools\Anaconda3\Scripts;C:\tools\Anaconda3;C:\tools\Anaconda3\Library\bin;%PATH%
and then run command which failed. In my case it was:
pip install conan
Anaconda uses separate python installation, and pip is also anaconda specific.
As Tokci said, it also works for Windows 7.
"Go with the mouse to the Windows Icon (lower left) and start typing "Anaconda". There should show up some matching entries. Select "Anaconda Prompt". A new command window, named "Anaconda Prompt" will open."
Then pip works.
The following also helped to import xgboost:
https://www.youtube.com/watch?v=05djBSOs1FA
If someone is using Arch Linux OS, I solved the TLS/SSL problem by running this:
sudo pacman -S openssl
Then I could use pip to install the package I needed:
pip install openpyxl
Go to Anaconda prompt and type (if you have python 3.x installed on your engine) :
py -m pip install pymysql
i was having the same issue and this solved my problem. later after doing this you can import pymysql in power shell or any other prompt.
The issue is due to OpenSSL package is missing on your PC.
If pip install openpyxl also gives error.
you can fix this by installing OpenSSL(Win64 OpenSSL v1.1.1g) from below site :
slproweb.com/products/Win32OpenSSL.html
Restart the IDE you are using, for changes to be in effect.
In Windows 10 SQL Server 19 the solution is known.
Copy the following files:
libssl-1_1-x64.dll
libcrypto-1_1-x64.dll
from the folder
C:\Program Files\Microsoft SQL Server\MSSSQL15.MSSQLSERVER\PYTHON_SERVICES\Library\bin
to the folder
C:\Program Files\Microsoft SQL Server\MSSSQL15.MSSQLSERVER\PYTHON_SERVICES\DLLs
Then open a new DOS command shell prompt.
From https://learn.microsoft.com/en-us/sql/machine-learning/troubleshooting/known-issues-for-sql-server-machine-learning-services?view=sql-server-ver15#7-unable-to-install-python-packages-using-pip-after-installing-sql-server-2019-on-windows
Worked for me.
pkg install openssl
Use this to enable ssl.
Currently there is same issue in Anaconda prompt (Anaconda3) on Windows 10. Here is workaround: https://github.com/ContinuumIO/anaconda-issues/issues/10576
Fixed this without having to change anything related to TSL/SSL.
I was trying to see if the same thing was happening to pip, and saw that pip was broken. Did some digging and realized it's probably caused by Homebrew deleted python#2 on February 1st, 2020.
Running brew uninstall python#2 to delete python2 installed by Homebrew.
Destroyed the virtual env created using python3 and created a new one. pip3 installing works fine again.
I am on macOS and I had used brew but what Vaulstein mentioned in his answer didn't cover my case.
I run the following commands to make sure my current python was not installed by brew
brew list | grep python
python
python#2
brew info python
python#3.8: stable 3.8.3 (bottled)
Interpreted, interactive, object-oriented programming language
https://www.python.org/
Not installed
...
So I download the latest 3.8.5 from https://www.python.org/ and when installing it I saw following information
Certificate verification and OpenSSL
This package includes its own private copy of OpenSSL 1.1.1. The
trust certificates in system and user keychains managed by the
Keychain Access application and the security command line utility are not used as defaults by the Python ssl module
After installed 3.8.5 it fixed the problem.
I got into this problem using Ubuntu, pyenv and Python 3.8.1 managed by pyenv. There was actually no way to get pip to work correctly, since every time I tried to install anything, including pip itself, the same error showed up.
Final solution was to install, via pyenv, a newer version, in this case 3.8.6. Apparently, from 3.8.4 Python is prepared to run SSL/TLS out of the box, so everything worked fine.
I simply solved the problem with following command:
brew upgrade python#3.9
SSL is included by default on this version!
In my case I was running into issues with my $PATH on Linux. This can also happen on MacOS.
Check to see if /usr/bin/pip3 install package_name_goes_here works for you. If so then run
which pip3 this will tell you which is the first directory that pip3 is installed in.
If it is something like /usr/local/bin/pip3 which is different from /usr/bin/pip3 then you may need to adjust your $PATH.
Run
echo $PATH and copy the result.
The PATH is simply a colon separated list of directories that contain directories. Bash will always return the first instance of the program that you are attempting to execute. Move all the system directories upfront. Here is a list of some of the system directories:
/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
If that fails then verify you have openssl installed by running openssl version -a if not then install openssl.
If you've installed anaconda via scoop, and encounter this error while using pip from within a conda environment you can resolve it by...
Adding these to your path
C:\Users\YOUR_USERNAME\scoop\apps\anaconda3\current
C:\Users\YOUR_USERNAME\scoop\apps\anaconda3\current\Scripts
C:\Users\YOUR_USERNAME\scoop\apps\anaconda3\current\Library
C:\Users\YOUR_USERNAME\scoop\apps\anaconda3\current\Library\bin
Installing openssl via scoop
scoop install openssl
And copying the following DLLs from ..\anaconda3\Library\bin to ..\anaconda3\DLLs
References:
https://stackoverflow.com/a/54897379
https://stackoverflow.com/a/60405693

Install python modules in mac osx

I am new to python. I am using python 3.5 on mac os x el capitan.
I tried using the command 'pip install requests' in the python interpreter IDLE. But it throws invalid 'syntax error'.
I read about installing modules is only possible in the command line.
So I moved to TERMINAL, but no command is working here also.
(I tried 'python -m pip install requests')
I read that mac os x comes with python 2.7 already installed and I ran 'easy_install pip' but it also works on the 2.7 version.
Then there's discussion about the PATH settings also.
Can please anybody explain to me how I can use my current version in TERMINAL window and what is the PATH scenario.
I am familiar with the environment variable settings and adding pythonpath in windows but not on mac.
Here is what you should do.
Use homebrew to install python 2.7 and 3.5 in a virtual environment.
pip install virtualenv
Then make a directory called virtualenvs in your root folder and add local files with.
cd virtualenvs
virtualenv venv
activate a virtualenv with source ~/virtualenvs/bin/activate
Then use pip to install brew in this virtualenv pip install brew
Then install python 2.7 as python and python 3 as python3:
brew update
brew install python
brew install python3
Then you can use python and python3 and not have to worry about the local install.
Then to run a file python3 filename.py
Followed this guide.
https://docs.python.org/3/using/mac.html
Found python3.5 in usr/local/bin instead of the default usr/bin where the default 2.7 exists.
The 3.5 Package automatically genrates an alias for itself that is python3.5 for use in terminal.
Ran the command 'python3.5 -m pip install requests' and everything went good.

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