Per https://github.com/cedadev/jasmin_scivm/issues/189

User should not need to run:

1. install-miniconda.sh
2. install-jaspy-env.sh

The running of (2) should automatically include (1) if not already up-to-date.

1. Add $SCRIPTDIR to all scripts and get python to work with this. - DONE

2. Create script: create-blank-env.sh - DONE

• use template

3. Script: add-envs-repo.sh - DONE

• cd top-level/../
• git clone
• cd jaspy/
• link ...

4. Script: list-jaspy-envs.sh - looks up all environments available, show as: - DONE

• py2.7 environments (under )
  • env 1
  • env 2 ...

5. See /doc/README.md for JASMIN docs

6. Move to Cedadev and move issues across

7. Review issues

8. Script: write-env-docs.sh <env_dir> <env_dir> <env_dir>

• environments/.../.../.md
• Environment:
• Install with: ----
  • Pkg: name , description, version, links...

9. Check users I previously told about JASMIN /apps/contrib/

Started with common.cfg.

More to do:

bin_dir=${JASPY_BASE_DIR}/jaspy/bin
bin_dir=${JASPY_BASE_DIR}/jaspy/miniconda_envs/jas${path_comps}/bin
bin_dir=${JASPY_BASE_DIR}/jaspy/miniconda_envs/jas${path_comps}/bin
bin_dir=${JASPY_BASE_DIR}/jaspy/miniconda_envs/jas${path_comps}/bin
bin_dir=${JASPY_BASE_DIR}/jaspy/miniconda_envs/jas${path_comps}/bin
bin_dir=${JASPY_BASE_DIR}/jaspy/miniconda_envs/${path_comps}/bin
bin_dir=${miniconda_env_dir}/bin

for binary in $(cat ${channel_urls_path} | grep http | sed 's|.*/||g'); do
for binary in $(cat ${channel_urls_path} | grep http | sed 's|.*/||g'); do

jaspy_version=$(echo $env_name | cut -d\- -f1)
jaspy_version=$(echo $env_name | cut -d\- -f1)

miniconda_env_dir=${JASPY_BASE_DIR}/jaspy/miniconda_envs/jas${path_comps}
miniconda_env_dir=${JASPY_BASE_DIR}/jaspy/miniconda_envs/${jaspy_version}/${miniconda_version}

miniconda_version=$(echo $env_name | cut -d\- -f2-3)
miniconda_version=$(echo $env_name | cut -d\- -f2-3)

path_comps=$(echo $channel_path | rev | cut -d/ -f1-2 | rev)
path_comps=$(echo $env_path | rev | cut -d/ -f2-3 | rev)
path_comps=$(echo $spec_dir | rev | cut -d/ -f2-3 | rev)
path_comps=$(echo $spec_dir | rev | cut -d/ -f2-3 | rev)
path_comps=$(echo $spec_dir | rev | cut -d/ -f2-3 | rev)
path_comps=$(echo $spec_file_dir | rev | cut -d/ -f2-3 | rev)
path_comps=$(echo $yaml_path | rev | cut -d/ -f2-3 | rev)

PLATFORM="linux-64"
PLATFORM=linux-64

• So that they are agnostic of the shell?
• So that load and unload would both work?

To automate, could do:

1. Capture env before activating
2. Run source activate <conda-env>
3. Capture env after activating
4. Diff the two envs
5. Put the changes in the envs into the ModuleFile directly (so that activation is not necessary).

Just do:

• change the environment file
• then run:
  conda-env update -f ../environment.yml

See:

/apps/contrib/jaspy/channels/jaspy3.6/m3-4.5.4/linux-64/.about.json

Fixed in: d9e86b8

Need to modify workflow to:

1. Input files: <env_name>-initial.yml
2. Process with:
   • get URLs: conda list --explicit | conda list --explicit | grep '^http'
   • put them into new YAML structure
   • insert header YAML
   • insert pip section
     • Use: full versions in pip
   • insert test section
3. Write to: <env_name>-spec.yml

To create an alias env:

1. We have env: "my-env-r20181022"
2. To create alias: "my-env-current":

• cd .../envs/
• ln -s my-env-r20181022 my-env-current

Then we will set up a separate ModuleFile for each:

• /apps/modulefiles/my-env/r20181022
• /apps/modulefiles/my-env/current

This means that "current" will be loaded by default if you do:

module load my-env

But you can specify a particular env with, e.g.:

module load my-env/r20181022
module load my-env/current

len("(jaspy3.6-m3-4.5.4-r20180816) [astephen@jasmin-cylc ~]$ ")
56

Gws/cedaproc/jaspy/channels

Per https://cds.climate.copernicus.eu/api-how-to

Examples of a simple module files:

$ cat /apps/modulefiles/jaspy2.7/tiny
#%Module -*- tcl -*-
##
## modulefile
##
proc ModulesHelp { } {
 puts stderr "\tAdds JASMIN Conda tools to your environment variables,"
}

module-whatis " Adds JASMIN Conda tools to your environment variables"

puts "source /apps/contrib/jaspy/bin/activate-this-env.sh jaspy2.7/tiny"

and

$ cat /apps/modulefiles/jaspy3.6/m3-4.5.4-r20180816
#%Module -*- tcl -*-
##
## modulefile
##
proc ModulesHelp { } {
 puts stderr "\tAdds JASMIN Conda tools to your environment variables,"
}

module-whatis " Adds JASMIN Conda tools to your environment variables"

puts "source /apps/contrib/jaspy/bin/activate-this-env.sh jaspy3.6/m3-4.5.4-r20180816"

And these use a script created from:

$ cat /vagrant-share/repos/jaspy/src/templates/activate-this-env.sh.tmpl
# Run with: source <activate-location> <env>

env_code=$1

env_search=$(echo $env_code | sed 's/\//\*/')
env_dir=$(find __JASPY_BASE_DIR__/jaspy/miniconda_envs/jaspy* -name "${env_search}")

env_name=$(basename $env_dir)
bin_dir=$(echo $env_dir | cut -d/ -f1-7)/bin

source ${bin_dir}/activate ${env_name}

See details in: https://github.com/agstephens/jaspy/blob/master/doc/README.md

opshome - dist - htdocs

AI can setup apache config file.

Otherwise there will be parsing issues due to different indentation decisions.

...it might fork or reuse this:

https://github.com/conda/conda-api/blob/master/conda_api.py

I suppose they can be...in that you can point to them as a single YAML file in a directory.

See this HTML page:

http://dist.ceda.ac.uk/jaspy/jaspy3.7/m3-4.5.11/

E.g.

 <tr>
      <td class="packagename"><a href="https://palletsprojects.com/p/click" alt="click">click</a></td>
      <td class="version">7.0</td>
      <td><a href="https://click.palletsprojects.com">doc</a></td>
      <td><a href="https://github.com/pallets/click">dev</a></td>
      <td class="tight">BSD-3-Clause</td>
<td>X</td><td></td>      <td class="summary">Python composable command line interface toolkit</td>
    </tr> 

1. E.g. An environment is defined as:

• Id: jaspy3.6-m3-4.5.4-r20180816
• Alias: jaspy3.6-v0.1.0

2. We try to resolve all dependencies...but

• some packages will conflict.

3. So, if this happens, we can do:
   i. Separate out the command-line tools (that conflict) into their own individual sub-envs, e.g.:
   • jaspy3.6-m3-4.5.4-r20180816-ncl with alias: jaspy3.6-v0.1.0-ncl