How to execute a batch script from an anaconda virtual environment (not from base)?

1
votes

I want to run a batch file in a Conda environment, not in the base env, but in another virtual environment (here pylayers). I copied the activate.bat script from F:\Anaconda3\Scripts to F:\Anaconda3\envs\pylayers\Scripts.

And my batch script (installer_win.bat) is:

call F:\Anaconda3\envs\pylayers\Scripts\activate.bat
conda install numpy --yes
conda install mayavi --yes
conda install shapely --yes
conda install libgdal --yes
conda install gdal --yes
conda install h5py --yes
conda install seaborn --yes
conda install PIL --yes
conda install basemap --yes
conda install wxpython --yes
conda install netCDF4 --yes
pip install protobuf 
pip install tqdm
pip install descartes
pip install bitstring
pip install geocoder
pip install triangle
pip install osmapi
pip install pyshp 
pip install Image
pip install pathos
pip install SimPy==2.2
pip install simplekml
pip install smopy

python setup.py install

When I execute the installer_win.bat file, it shows the following behavior:

Output: #stops after executing very first line in the batch file.
(base) C:\Users\mkdth>activate pylayers

(pylayers) C:\Users\mkdth>cd /d F:\Pycharm\Projects\pylayers-master

(pylayers) F:\Pycharm\Projects\pylayers-master>installer_win.bat

(pylayers) F:\Pycharm\Projects\pylayers-master>call F:\Anaconda3\envs\pylayers\Scripts\activate.bat
The system cannot find the path specified.

(pylayers) F:\Pycharm\Projects\pylayers-master>conda install numpy --yes
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: F:\Anaconda3\envs\pylayers

  added / updated specs:
    - numpy


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    openssl-1.1.1g             |       he774522_0         4.8 MB
    ------------------------------------------------------------
                                           Total:         4.8 MB

The following NEW packages will be INSTALLED:

  numpy-base         pkgs/main/win-64::numpy-base-1.18.1-py36hc3f5095_1

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2020.4.5~ --> pkgs/main::ca-certificates-2020.1.1-0
  certifi            conda-forge::certifi-2020.4.5.2-py36h~ --> pkgs/main::certifi-2020.4.5.1-py36_0
  numpy              conda-forge::numpy-1.18.5-py36h4d86e3~ --> pkgs/main::numpy-1.18.1-py36h93ca92e_0
  openssl                                       conda-forge --> pkgs/main



Downloading and Extracting Packages
openssl-1.1.1g       | 4.8 MB    | ############################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

(pylayers) F:\Pycharm\Projects\pylayers-master>

I also tried to modify the batch file to activate pylayers environment from the base env and run the conda or pip commands one by one, but it installs to base environment only. See the bat script

Attempt 1

Installer_win.bat file: 

call F:\Anaconda3\Scripts\activate.bat
activate pylayers
pause
conda install numpy --yes
conda install mayavi --yes
conda install shapely --yes
conda install libgdal --yes
conda install gdal --yes
conda install h5py --yes
conda install seaborn --yes
conda install PIL --yes
conda install basemap --yes
conda install wxpython --yes
conda install netCDF4 --yes
pip install protobuf 
pip install tqdm
pip install descartes
pip install bitstring
pip install geocoder
pip install triangle
pip install osmapi
pip install pyshp 
pip install Image
pip install pathos
pip install SimPy==2.2
pip install simplekml
pip install smopy

python setup.py install

Output: activates pylayers env and stops

(pylayers) F:\Pycharm\Projects\pylayers-master>installer_win.bat

(pylayers) F:\Pycharm\Projects\pylayers-master>call F:\Anaconda3\Scripts\activate.bat

(base) F:\Pycharm\Projects\pylayers-master>activate pylayers

(pylayers) F:\Pycharm\Projects\pylayers-master>

Attempt2:

Installer_win.bat file: 

call F:\Anaconda3\Scripts\activate.bat
activate pylayers
conda install numpy --yes
conda install mayavi --yes
conda install shapely --yes
conda install libgdal --yes
conda install gdal --yes
conda install h5py --yes
conda install seaborn --yes
conda install PIL --yes
conda install basemap --yes
conda install wxpython --yes
conda install netCDF4 --yes
pip install protobuf 
pip install tqdm
pip install descartes
pip install bitstring
pip install geocoder
pip install triangle
pip install osmapi
pip install pyshp 
pip install Image
pip install pathos
pip install SimPy==2.2
pip install simplekml
pip install smopy

python setup.py install

Output: #activates base env and stops

(pylayers) F:\Pycharm\Projects\pylayers-master>installer_win.bat

(pylayers) F:\Pycharm\Projects\pylayers-master>call F:\Anaconda3\Scripts\activate.bat

(base) F:\Pycharm\Projects\pylayers-master>activate pylayers

Attempt 3

Installer_win.bat file: 

call F:\Anaconda3\Scripts\activate.bat
conda install numpy --yes
conda install mayavi --yes
conda install shapely --yes
conda install libgdal --yes
conda install gdal --yes
conda install h5py --yes
conda install seaborn --yes
conda install PIL --yes
conda install basemap --yes
conda install wxpython --yes
conda install netCDF4 --yes
pip install protobuf 
pip install tqdm
pip install descartes
pip install bitstring
pip install geocoder
pip install triangle
pip install osmapi
pip install pyshp 
pip install Image
pip install pathos
pip install SimPy==2.2
pip install simplekml
pip install smopy

python setup.py install

Output: #starts installing in base env

(pylayers) F:\Pycharm\Projects\pylayers-master>installer_win.bat

(pylayers) F:\Pycharm\Projects\pylayers-master>call F:\Anaconda3\Scripts\activate.bat

(base) F:\Pycharm\Projects\pylayers-master>activate pylayers

(pylayers) F:\Pycharm\Projects\pylayers-master>installer_win.bat

(pylayers) F:\Pycharm\Projects\pylayers-master>call F:\Anaconda3\Scripts\activate.bat

(base) F:\Pycharm\Projects\pylayers-master>conda install numpy --yes
Collecting package metadata (current_repodata.json): failed

CondaError: KeyboardInterrupt

^CTerminate batch job (Y/N)?
^C

Can someone help me to run this batch file under a Conda virtual env, please?

Any suggestions would be very much appreciated.

2
batch-filepipanacondacondavirtual-environment
Please revisit your question and format it properly, that is not just the code/content of the batch file! - Compo
Is there any other aim for this script other than installing stuff? If not, I would recommend putting all of this into a YAML environment definition (and yes it can also install local stuff - see Advanced Pip Example), then simply run conda env update -n pylayers -f env.yaml. Otherwise, to execute arbitrary scripts in an env there is conda run -n pylayers installer_win.bat. - merv
As conda is a batch file, should each one of those commands not be proceeded by call? - Compo
thanks @merv "conda run -n pylayers installer_win.bat" worked. So do the 'conda env update -n pylayers -f env.yml' idea. - thangaraj m.d
Okay, I wrote it up as an answer proper. - merv

2 Answers

2
votes

There are two ways to go. I think the first is the cleaner way to go.

Option 1: YAML Definition

If the entire procedure is only for installations, it can be condensed into a single YAML environment definition and executed in a one go. This includes the local package installation, which for the current example I'll call foo.

foo_install.yaml

name: foo_install
channels:
  - defaults
dependencies:
  - numpy
  - mayavi
  - shapely
  - libgdal
  - gdal
  - h5py
  - seaborn
  - PIL
  - basemap
  - wxpython
  - netCDF4
  - pip
  - pip:
    - protobuf
    - tqdm
    - descartes
    - bitstring
    - geocoder
    - triangle
    - osmapi
    - pyshp
    - Image
    - pathos
    - SimPy==2.2
    - simplekml
    - smopy
    - -e ./../foo  # this assumes running from inside the `foo` folder

To install this into an arbitrary env (e.g., pylevels) as an addition to the env, one would use

conda env update -n pylevels -f foo_install.yaml

where this is run from within the foo folder.

See the Advanced Pip Example for a showcase of other options (basically, everything pip install accepts can be included in a YAML file).

Option 2: conda run

More generically, one can run arbitrary scripts inside a specific environment by using conda run. This avoids having to include activation commands inside scripts themselves. In this case, you could run your script with

conda run -n pylevels installer_win.bat

I would only resort to this if you need to also configure some environment variables or something similar. In that case, I would still make the YAML, and reduce all the installation to the single line:

installer_win.bat

conda env update -f foo_install.yaml

and include further actions after that.

0
votes

To run a bat file from a dos prompt inside a new (non-base) conda env, you can try something like this:

prompt> cmd "/c activate ds_tensorflow && myfile.bat && deactivate"

contents of myfile.bat to show you are in the non-base env:

echo hello
python -c "import sys; print(sys.version)"

You can replace myfile.bat in the >> line above with your bat file. This will also work without the bat file, just run each command within the /c activate .... deactivate wrapper.

cmd "/c activate ds_tensorflow && python -c "import sys; print(sys.version)" && deactivate"