Develop Reference

Conda can't install packages from requirements.txt available in conda-forge, although package exists in conda-forge

I added conda-forge to the conda channels:
$ conda config --show channels
channels:
- conda-forge
- defaults
my requirements.txt contains, among others, these lines:
ipython-genutils==0.2.0
jupyter-client==6.1.12
jupyterlab-pygments==0.1.2
appnope==0.1.2
jupyterlab-widgets==1.0.0
data==0.4
prometheus-client==0.11.0
latex==0.7.0
scipy==1.5.4
jupyter-core==4.7.1
jupyter-console==6.4.0
async-generator==1.10
vg==1.10.0
sklearn==0.0
postgis==1.0.4
When I try to create a new environment from this requirements.txt using conda with
conda create --name myenv --file requirements.txt
I get the following errors:
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- ipython-genutils==0.2.0
- jupyter-client==6.1.12
- jupyterlab-pygments==0.1.2
- appnope==0.1.2
- jupyterlab-widgets==1.0.0
- data==0.4
- prometheus-client==0.11.0
- latex==0.7.0
- scipy==1.5.4
- jupyter-core==4.7.1
- jupyter-console==6.4.0
- async-generator==1.10
- vg==1.10.0
- sklearn==0.0
- postgis==1.0.4
Current channels:
- https://conda.anaconda.org/conda-forge/linux-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
As you can see, conda-forge is listed under "current channels" and ipython-genutils==0.2.0 is available in conda-forge. However, the package is not found. How can I fix this problem?
I tried both conda config --set channel_priority flexible and ... stable
I run Ubuntu 20.04 LTS, Python 3.10 and Conda 4.12.0

It looks to me like this should have been a requirements.txt to be used by pip. Note that conda packages can have slightly different names than what is available on pypi.
ipython-genutils is not the correct name, looking at the link you have provided, the name of the package is ipython_genutils with an underscore. The same is true for the other packages that you have written with a hyphen. They should all be spelled with an underscore.
That leaves
- sklearn==0.0
- latex==0.7.0
- vg==1.10.0
- scipy==1.5.4
- postgis==1.0.4
- data==0.4
- appnope==0.1.2
sklearn==0.0 seems to be a corrupt line in your file. The package's name is scikit-learn. latex, vg and data are not available on conda channels as far as I can tell. The same goes for scipy==1.5.4, only 1.5.3 and 1.6 are available. postgis only goes back to 2.4.3 on conda-forge , see here, but also seems to be different from what is available on pypi. appnope is a package only available for macOS, see it's description:
Simple package for disabling App Nap on macOS >= 10.9, which can be problematic.
So with that in mind, we can create a yml file that installs from both conda channels and from pip (Changes to your file: replaced - with _, removed appnope, added pip dependency, renamed sklearn to scikit-learn and moved it together with latex, scipy, vg, data, postgis to pip requirements. If you are flexible with scipy==1.5.4, I would advise to change it to scipy==1.5.3 or scipy==1.6.0 and move scipy and sklearn out of the pip installed packages):
name: myenv
dependencies:
- ipython_genutils==0.2.0
- jupyter_client==6.1.12
- jupyterlab_pygments==0.1.2
- jupyterlab_widgets==1.0.0
- prometheus_client==0.11.0
- jupyter_core==4.7.1
- jupyter_console==6.4.0
- async_generator==1.10
- pip
- pip:
- scikit-learn
- latex==0.7.0
- scipy==1.5.4
- vg==1.10.0
- data==0.4.0
- postgis==1.0.4
Save this as environment.yml and then do
conda env create -f environment.yml

conda install and conda build result in different dependency versions

I'm trying to build a package which includes h5py. When using conda build, it seems to install the wrong version of the dependency. It installs 3.2.1-py37h6c542dc_0, which includes hdf5: 1.10.6-nompi_h6a2412b_1114.
The problem is that this hdf5 lib, seems to have these setting:
(Read-Only) S3 VFD: yes
This causes an error for me. When just running conda install h5py==3.2.1, it does install the right version (hdf5-1.10.6-nompi_h3c11f04_101).
Why is there a difference?

"Why is there a difference?
Using conda install h5py=3.2.1 additionally includes all the previous constraints in the current environment, whereas during a conda build run, a new environment is created only with requirements that the package specifies. That is, it is more like running conda create -n foo h5py=3.2.1.
So, that covers the mechanism, but we can also look at the particular package dependencies to see why the current environment constrains to the older hdf5-1.10.6-nompi_h3c11f04_101, which OP states is preferred. Here is the package info for the two:
hdf5-1.10.6-nompi_h6a2412b_1114
$ mamba search --info conda-forge/linux-64::hdf5[version='1.10.6',build='nompi_h6a2412b_1114']
hdf5 1.10.6 nompi_h6a2412b_1114
-------------------------------
file name : hdf5-1.10.6-nompi_h6a2412b_1114.tar.bz2
name : hdf5
version : 1.10.6
build : nompi_h6a2412b_1114
build number: 1114
size : 3.1 MB
license : LicenseRef-HDF5
subdir : linux-64
url : https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.10.6-nompi_h6a2412b_1114.tar.bz2
md5 : 0a2984b78f51148d7ff6219abe73509e
timestamp : 2021-01-08 23:10:11 UTC
dependencies:
- libcurl >=7.71.1,<8.0a0
- libgcc-ng >=9.3.0
- libgfortran-ng
- libgfortran5 >=9.3.0
- libstdcxx-ng >=9.3.0
- openssl >=1.1.1i,<1.1.2a
- zlib >=1.2.11,<1.3.0a0
hdf5-1.10.6-nompi_h3c11f04_101
$ mamba search --info conda-forge/linux-64::hdf5[version='1.10.6',build='nompi_h3c11f04_101']
hdf5 1.10.6 nompi_h3c11f04_101
------------------------------
file name : hdf5-1.10.6-nompi_h3c11f04_101.tar.bz2
name : hdf5
version : 1.10.6
build : nompi_h3c11f04_101
build number: 101
size : 3.0 MB
license : HDF5
subdir : linux-64
url : https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.10.6-nompi_h3c11f04_101.tar.bz2
md5 : 9f1ccc4d36edf8ea15ce19f52cf6d601
timestamp : 2020-07-31 12:26:29 UTC
dependencies:
- libgcc-ng >=7.5.0
- libgfortran-ng >=7,<8.0a0
- libstdcxx-ng >=7.5.0
- zlib >=1.2.11,<1.3.0a0
The difference here is that the latter works with older versions of libgcc-ng, libstdcxx-ng, and libgfortran-ng (below 9.3.0), as well as has no constraint on openssl or libcurl. So, we can guess that the current environment where the conda install h5py=3.2.1 was invoked has one of these restrictions.

How to install fiona 1.6?

I am trying to install fiona=1.6 but I get the following error
conda install fiona=1.6
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Collecting package metadata: done
Solving environment: -
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- conda-forge/noarch::flask-cors==3.0.7=py_0
- conda-forge/osx-64::blaze==0.11.3=py36_0
- conda-forge/noarch::flask==1.0.2=py_2
failed
PackagesNotFoundError: The following packages are not available from current channels:
- fiona=1.6 -> gdal==1.11.4
Current channels:
- https://conda.anaconda.org/conda-forge/osx-64
- https://conda.anaconda.org/conda-forge/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
If I try to install gdal==1.11.4, I get the following
conda install -c conda-forge gdal=1.11.4
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Collecting package metadata: done
Solving environment: |
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- conda-forge/noarch::flask-cors==3.0.7=py_0
- conda-forge/osx-64::blaze==0.11.3=py36_0
- conda-forge/noarch::flask==1.0.2=py_2
failed
PackagesNotFoundError: The following packages are not available from current channels:
- gdal=1.11.4
Current channels:
- https://conda.anaconda.org/conda-forge/osx-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/free/osx-64
- https://repo.anaconda.com/pkgs/free/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
This is the result of conda info
conda info
active environment : base
active env location : /anaconda3
shell level : 1
user config file : /Users/massaro/.condarc
populated config files : /Users/massaro/.condarc
conda version : 4.6.11
conda-build version : 3.17.8
python version : 3.6.8.final.0
base environment : /anaconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /anaconda3/pkgs
/Users/massaro/.conda/pkgs
envs directories : /anaconda3/envs
/Users/massaro/.conda/envs
platform : osx-64
user-agent : conda/4.6.11 requests/2.21.0 CPython/3.6.8 Darwin/17.5.0 OSX/10.13.4
UID:GID : 502:20
netrc file : None

Python Versions
The Conda Forge channel only has gdal v1.11.4 for Python 2.7, 3.4, and 3.5. You either need to use a newer version of Fiona (current is 1.8) or make a new env that includes one of those older Python versions.
For example,
conda create -n fiona_1_6 fiona=1.6 python=3.5
Channel defaults is Required
Another issue you face is that you have removed the defaults channel from your configuration (as per your conda info). It is impossible to install fiona=1.6 with only the conda-forge channel. My recommendation would be to have both conda-forge and defaults in your configuration, but just set conda-forge to have higher priority (if that's what you want). You can do this like so,
conda config --append channels defaults
If you really don't want to include defaults, but just want a temporary workaround, then you can simply run the first command with a --channels | -c flag
conda create -n fiona_1_6 -c conda-forge -c defaults fiona=1.6 python=3.5
This will still give conda-forge precedence, but allow missing dependencies to be sourced from defaults.
Environment File
If you have more than just Fiona that you require, it may be cleaner to put together a requirements file, like so
fiona_1_6.yaml
name: fiona_1_6
channels:
- conda-forge
- defaults
dependencies:
- python=3.5
- fiona=1.6
- osmnx
Then create the new environment with this:
conda env create -f fiona_1_6.yaml

Doing what the error message told me to,
To search for alternate channels that may provide the conda package you're
looking for, navigate to https://anaconda.org
and typing in gdal in the search box led me to https://anaconda.org/conda-forge/gdal which has this installation instruction:
conda install -c conda-forge gdal=1.11.4
Try that to install the gdal dependency, maybe?

Conda can't find packages at pypi.org/simple

I have a problem with installing packages via conda. It can not find any package in channel https://pypi.org simple.
conda install logbook
returns:
PS C:\WINDOWS\system32> conda config --add channels
https://pypi.org/simple
Warning: 'https://pypi.org/simple' already in 'channels' list, moving to the top
PS C:\WINDOWS\system32> conda install Logbook
Fetching package metadata ....
WARNING: The remote server could not find the noarch directory for the
requested channel with url: https://pypi.org/simple
It is possible you have given conda an invalid channel. Please double-check
your conda configuration using `conda config --show`.
If the requested url is in fact a valid conda channel, please request that the
channel administrator create `noarch/repodata.json` and associated
`noarch/repodata.json.bz2` files, even if `noarch/repodata.json` is empty.
$ mkdir noarch
$ echo '{}' > noarch/repodata.json
$ bzip2 -k noarch/repodata.json
...........
PackageNotFoundError: Packages missing in current channels:
- logbook
We have searched for the packages in the following channels:
- https://pypi.org/simple/win-64
- https://pypi.org/simple/noarch
- https://repo.continuum.io/pkgs/main/win-64
- https://repo.continuum.io/pkgs/main/noarch
- https://repo.continuum.io/pkgs/free/win-64
- https://repo.continuum.io/pkgs/free/noarch
- https://repo.continuum.io/pkgs/r/win-64
- https://repo.continuum.io/pkgs/r/noarch
- https://repo.continuum.io/pkgs/pro/win-64
- https://repo.continuum.io/pkgs/pro/noarch
- https://repo.continuum.io/pkgs/msys2/win-64
- https://repo.continuum.io/pkgs/msys2/noarch
I have checked manually in browser, that the logbook module is in the list on page https://pypi.org/simple.
hoever, it seems that conda seeks packages in https://pypi.org/simple/win-64, but the win-64 directory does not exist there.
conda config --show says, that configured channel is https://pypi.org/simple
add_anaconda_token: True
add_pip_as_python_dependency: True
allow_non_channel_urls: True
allow_softlinks: False
always_copy: False
always_softlink: False
always_yes: False
anaconda_upload: None
auto_update_conda: True
changeps1: True
channel_alias: https://conda.anaconda.org
channel_priority: True
channels:
- https://pypi.org/simple
- https://pypi.org/simple/
- defaults
client_ssl_cert: None
client_ssl_cert_key: None
clobber: False
create_default_packages: []
custom_channels:
pkgs/main: https://repo.continuum.io/
pkgs/free: https://repo.continuum.io/
pkgs/r: https://repo.continuum.io/
pkgs/pro: https://repo.continuum.io/
pkgs/msys2: https://repo.continuum.io/
C:/Program%20Files/Anaconda3/conda-bld: file:///
Any advice?

A conda channel has to have a specific layout (win-64, win-32, ...) and the package has to be built in a conda-specific way (see Building conda packages with conda skeleton). The packages are generally build against specific Python versions (although there should also be noarch packages) and/or numpy versions and for different platforms (windows, linux, mac 32bit or 64bit).
You cannot directly install packages from PyPI using conda because PyPI doesn't qualify as conda-channel and even if it were the packages there aren't build like conda-packages. But you can install them using pip (within conda).
But: You could check if the packages you want are distributed in a conda-conforming channel (a very popular channel currently is conda-forge). At a first glance several channels contain a package named logbook in the anaconda cloud (search results for logbook).
If you find a channel that distributes the desired version of your package (and against the desired Python version and platform) then just use:
conda install -c channel_name logbook

Many Python products are available for Windows on the Gohlke page.
Assuming you have 64-bit Py3.6 installed in its own environment, called Py36, you can do this.
Download Logbook-1.1.0-cp36-cp36m-win_amd64.whl from Gohlke (or whatever version it is that you need).
Then within a command prompt:
activate the conda environment where you want to install Logbook.
Use pip to install the whl that you have downloaded within that environment.
Verify success, if you wish.
C:\scratch>activate Py36
(Py36) C:\scratch>pip install Logbook-1.1.0-cp36-cp36m-win_amd64.whl
Processing c:\scratch\logbook-1.1.0-cp36-cp36m-win_amd64.whl
Installing collected packages: Logbook
Successfully installed Logbook-1.1.0
(Py36) C:\scratch>conda list
# packages in environment at C:\ProgramData\Miniconda3\envs\Py36:
#
beautifulsoup4 4.6.0 <pip>
certifi 2017.11.5 py36hb8ac631_0
chardet 3.0.4 <pip>
idna 2.6 <pip>
Logbook 1.1.0 <pip>
opencv-python 3.4.0+contrib <pip>
pip 9.0.1 py36h226ae91_4
python 3.6.3 h3b118a2_4
requests 2.18.4 <pip>
setuptools 36.5.0 py36h65f9e6e_0
urllib3 1.22 <pip>
vc 14 h2379b0c_2
vs2015_runtime 14.0.25123 hd4c4e62_2
wheel 0.30.0 py36h6c3ec14_1
wikipedia 1.4.0 <pip>
wincertstore 0.2 py36h7fe50ca_0
Edit: Answer to query in comment.
I entered this:
conda env export -n Py36 -f Py36.yml
Content of yaml file.
name: Py36
channels:
- defaults
dependencies:
- certifi=2017.11.5=py36hb8ac631_0
- pip=9.0.1=py36h226ae91_4
- python=3.6.3=h3b118a2_4
- setuptools=36.5.0=py36h65f9e6e_0
- vc=14=h2379b0c_2
- vs2015_runtime=14.0.25123=hd4c4e62_2
- wheel=0.30.0=py36h6c3ec14_1
- wincertstore=0.2=py36h7fe50ca_0
- pip:
- beautifulsoup4==4.6.0
- chardet==3.0.4
- idna==2.6
- logbook==1.1.0
- opencv-python==3.4.0+contrib
- requests==2.18.4
- urllib3==1.22
- wikipedia==1.4.0
prefix: C:\ProgramData\Miniconda3\envs\Py36

Downgrade Python to 3.5 - conflict with ppft/xz

I would like to downgrade Python from 3.6 to 3.5. conda tells me the following:
$ conda install python=3.5.0 -n myenv
Fetching package metadata .........
Solving package specifications: .
UnsatisfiableError: The following specifications were found to be in conflict:
- ppft -> python 3.6* -> xz 5.2.*
- python 3.5.0*
Now knowing any of the packages in the first line, conda info ppft gives me ResolvePackageNotFound. conda info xz gives me a long list of versions, the latest of which is
xz 5.2.3 0
----------
file name : xz-5.2.3-0.tar.bz2
name : xz
version : 5.2.3
build string: 0
build number: 0
channel : defaults
size : 667 KB
arch : x86_64
date : 2017-08-18
license : Public-Domain, GPL
license_family: GPL2
md5 : 585458787b315ac1e5fb3a1ee71cad75
noarch : None
platform : linux
url : https://repo.continuum.io/pkgs/free/linux-64/xz-5.2.3-0.tar.bz2
dependencies:
How do I continue - what's going on?

First off ppft is not listed in the default anaconda directory but in conda-forge. But if you take a look at the files in that directory you will find there are versions for python 3.5. Furthermore according to the homepage for xz, it is compatible with python 2 or 3.
One option would be to remove the conflicting libraries, downgrade to 3.5, and then reinstall the libraries later. For example
conda uninstall ppft xz
conda install python=3.5 -n myenv
conda install xz
conda install -c conda-forge ppft