Remove ncl and its dependencies from main dependencies and add documentation how to install it

[valeriupredoi]

Description

• Closes Bringing our environment to modern standards (also with removal of NCL) #3812
• Link to documentation: TBA

---

On my local machine:

(base) valeriu@valeriu-PORTEGE-Z30-C:~/ESMValTool$ \time mamba env create -n noNCL -f environment.yml

209.47user 41.62system 4:02.07elapsed 103%CPU (0avgtext+0avgdata 3208236maxresident)k                                                                    
2630240inputs+8222704outputs (4851major+1880442minor)pagefaults 0swaps

then, once the env is created and activated, if one needs NCL:

(noNCL) valeriu@valeriu-PORTEGE-Z30-C:~/ESMValTool$ \time conda install -c conda-forge ncl
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/valeriu/miniconda3/envs/noNCL

  added / updated specs:
    - ncl


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    hdfeos5-5.1.16             |      h51d0b48_17         466 KB  conda-forge
    libntlm-1.8                |       hb9d3cd8_0          33 KB  conda-forge
    poppler-24.12.0            |       hd7b24de_2         1.8 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         2.3 MB

The following NEW packages will be INSTALLED:

  cfitsio            conda-forge/linux-64::cfitsio-4.4.1-ha728647_2 
  cmor               conda-forge/linux-64::cmor-3.9.0-py312h5d372d2_1 
  cyrus-sasl         conda-forge/linux-64::cyrus-sasl-2.1.27-h54b06d7_7 
  fmt                conda-forge/linux-64::fmt-11.0.2-h434a139_0 
  gettext            conda-forge/linux-64::gettext-0.22.5-he02047a_3 
  gettext-tools      conda-forge/linux-64::gettext-tools-0.22.5-he02047a_3 
  gsl                conda-forge/linux-64::gsl-2.7-he838d99_0 
  hdfeos2            conda-forge/linux-64::hdfeos2-2.20-h3e53b52_1004 
  hdfeos5            conda-forge/linux-64::hdfeos5-5.1.16-h51d0b48_17 
  kealib             conda-forge/linux-64::kealib-1.5.3-hf8d3e68_2 
  libasprintf        conda-forge/linux-64::libasprintf-0.22.5-he8f35ee_3 
  libasprintf-devel  conda-forge/linux-64::libasprintf-devel-0.22.5-he8f35ee_3 
  libgdal            conda-forge/linux-64::libgdal-3.9.2-ha770c72_7 
  libgdal-fits       conda-forge/linux-64::libgdal-fits-3.9.2-h2db6552_7 
  libgdal-grib       conda-forge/linux-64::libgdal-grib-3.9.2-hc3b29a1_7 
  libgdal-hdf4       conda-forge/linux-64::libgdal-hdf4-3.9.2-hd5ecb85_7 
  libgdal-hdf5       conda-forge/linux-64::libgdal-hdf5-3.9.2-h6283f77_7 
  libgdal-jp2openjp~ conda-forge/linux-64::libgdal-jp2openjpeg-3.9.2-h1b2c38e_7 
  libgdal-kea        conda-forge/linux-64::libgdal-kea-3.9.2-h1df15e4_7 
  libgdal-netcdf     conda-forge/linux-64::libgdal-netcdf-3.9.2-hf2d2f32_7 
  libgdal-pdf        conda-forge/linux-64::libgdal-pdf-3.9.2-h600f43f_7 
  libgdal-pg         conda-forge/linux-64::libgdal-pg-3.9.2-h5e77dd0_7 
  libgdal-postgisra~ conda-forge/linux-64::libgdal-postgisraster-3.9.2-h5e77dd0_7 
  libgdal-tiledb     conda-forge/linux-64::libgdal-tiledb-3.9.2-h4a3bace_5 
  libgdal-xls        conda-forge/linux-64::libgdal-xls-3.9.2-h03c987c_7 
  libgettextpo       conda-forge/linux-64::libgettextpo-0.22.5-he02047a_3 
  libgettextpo-devel conda-forge/linux-64::libgettextpo-devel-0.22.5-he02047a_3 
  libntlm            conda-forge/linux-64::libntlm-1.8-hb9d3cd8_0 
  libpq              conda-forge/linux-64::libpq-17.2-h04577a9_0 
  ncl                conda-forge/linux-64::ncl-6.6.2-h7cb714c_54 
  nspr               conda-forge/linux-64::nspr-4.36-h5888daf_0 
  nss                conda-forge/linux-64::nss-3.107-hdf54f9c_0 
  openblas           conda-forge/linux-64::openblas-0.3.28-pthreads_h6ec200e_1 
  openldap           conda-forge/linux-64::openldap-2.6.9-he970967_0 
  poppler            conda-forge/linux-64::poppler-24.12.0-hd7b24de_2 
  poppler-data       conda-forge/noarch::poppler-data-0.4.12-hd8ed1ab_0 
  postgresql         conda-forge/linux-64::postgresql-17.2-h1122569_0 
  spdlog             conda-forge/linux-64::spdlog-1.14.1-hed91bc2_1 
  tiledb             conda-forge/linux-64::tiledb-2.26.1-h4c922dd_1 
  tzcode             conda-forge/linux-64::tzcode-2024b-hb9d3cd8_0 
  xorg-imake         conda-forge/linux-64::xorg-imake-1.0.10-h5888daf_0 
  xorg-libxaw        conda-forge/linux-64::xorg-libxaw-1.0.16-hb9d3cd8_0 
  xorg-libxmu        conda-forge/linux-64::xorg-libxmu-1.2.1-hb9d3cd8_1 
  xorg-libxpm        conda-forge/linux-64::xorg-libxpm-3.5.17-hb9d3cd8_1 
  xorg-makedepend    conda-forge/linux-64::xorg-makedepend-1.0.9-h59595ed_0 

The following packages will be DOWNGRADED:

  cdo                                      2.4.4-h0e6046d_2 --> 2.4.4-hbe50dc4_0 
  esmf                               8.7.0-nompi_h4441c20_1 --> 8.4.2-nompi_h9e768e6_3 
  esmpy                                  8.7.0-pyhecae5ae_1 --> 8.4.2-pyhc1e730c_4 
  fiona                              1.10.1-py312h02b19dd_3 --> 1.10.1-py312h5aa26c2_1 
  gdal                              3.10.0-py312hc55c449_13 --> 3.9.2-py312h1299960_7 
  geos                                    3.13.0-h5888daf_0 --> 3.12.2-he02047a_1 
  geotiff                                  1.7.3-h77b800c_3 --> 1.7.3-hf7fa9e8_2 
  imagecodecs                     2024.9.22-py312hf6703b6_0 --> 2024.6.1-py312h6d9a048_4 
  json-c                                    0.18-h6688a6e_0 --> 0.17-h1220068_1 
  libdeflate                                1.22-hb9d3cd8_0 --> 1.21-h4bc722e_0 
  libgdal-core                            3.10.0-h7250d82_6 --> 3.9.2-hbd1db40_2 
  librttopo                               1.1.0-h97f6797_17 --> 1.1.0-hc670b87_16 
  libspatialite                           5.1.0-h1b4f908_12 --> 5.1.0-h15fa968_9 
  libtiff                                  4.7.0-hc4654cb_2 --> 4.7.0-h6565414_0 
  magics                                  4.15.5-hc87abea_0 --> 4.15.4-h24e9adf_1 
  proj                                     9.5.1-h0054346_0 --> 9.4.1-h54d7996_1 
  pyproj                              3.7.0-py312he630544_0 --> 3.6.1-py312h9211aeb_9 
  rasterio                            1.4.3-py312h8cae83d_0 --> 1.3.11-py312hd177ed6_1 
  shapely                             2.0.6-py312h391bc85_2 --> 2.0.6-py312h6cab151_1 
  xesmf                                  0.8.8-pyhd8ed1ab_1 --> 0.8.7-pyhd8ed1ab_0 


Proceed ([y]/n)?

and timing for that is very reasonable:

54.50user 8.13system 1:28.96elapsed 70%CPU (0avgtext+0avgdata 3369900maxresident)k
1878328inputs+892560outputs (27major+1376394minor)pagefaults 0swaps

So the user who needs NCL can just install it in the already created ESMValTool environment; of course, quite a few dependencies will be downgraded (and remember that even Python will be downgraded to 3.12 if the env is built with 3.13) but this is a lot more of an elegant and efficient solution for us, then to keep dragging NCL along with us!

The other two deps - imagemagick and nco can be installed together with ncl in one call or separately, I am doing separately to see which deps modify each:

(noNCL) valeriu@valeriu-PORTEGE-Z30-C:~/ESMValTool$ conda install -c conda-forge imagemagick
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/valeriu/miniconda3/envs/noNCL

  added / updated specs:
    - imagemagick


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    imagemagick-7.1.1_43       |imagemagick_hf2058d9_2         2.2 MB  conda-forge
    libheif-1.19.5             | gpl_hc21c24c_100         575 KB  conda-forge
    libwebp-1.5.0              |       hae8dbeb_0          90 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         2.8 MB

The following NEW packages will be INSTALLED:

  ghostscript        conda-forge/linux-64::ghostscript-10.04.0-h5888daf_0 
  imagemagick        conda-forge/linux-64::imagemagick-7.1.1_43-imagemagick_hf2058d9_2 
  jbig               conda-forge/linux-64::jbig-2.1-h7f98852_2003 
  libwebp            conda-forge/linux-64::libwebp-1.5.0-hae8dbeb_0 
  pkg-config         conda-forge/linux-64::pkg-config-0.29.2-h4bc722e_1009 

The following packages will be UPDATED:

  libheif                           1.18.2-gpl_hffcb242_100 --> 1.19.5-gpl_hc21c24c_100

and

(noNCL) valeriu@valeriu-PORTEGE-Z30-C:~/ESMValTool$ conda install -c conda-forge nco
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/valeriu/miniconda3/envs/noNCL

  added / updated specs:
    - nco


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    nco-5.3.0                  |       hf7c1f58_0         1.8 MB  conda-forge
    tempest-remap-2.2.0        |       heeae502_5         965 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         2.7 MB

The following NEW packages will be INSTALLED:

  nco                conda-forge/linux-64::nco-5.3.0-hf7c1f58_0 
  tempest-remap      conda-forge/linux-64::tempest-remap-2.2.0-heeae502_5

both easy to have them installed!

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