Merge pull request #130 from Exabyte-io/epic/SOF-7450

Epic/sof 7450 - AlmaLinux Updates - - Tracking in `SOF-7660`

Author: timurbazhirov

applications/jupyterLab.yml

@@ -1,10 +1,10 @@
 name: jupyterLab
 shortName: jl
 summary: JupyterLab
-defaultVersion: '3.0.3'
+defaultVersion: '4.3.0'
 versions:
-  - version: '3.0.3'
+  - version: '4.3.0'
     isDefault: true
   - version: '3.0.3'
-    isDefault: false
+  - version: '3.0.3'
     build: with-pre-installed-packages

applications/python.yml

@@ -1,11 +1,13 @@
 name: python
 shortName: py
 summary: Python Script
-defaultVersion: '3.8.6'
+defaultVersion: '3.10.13'
 versions:
-  - version: '3.6.12'
-  - version: '3.7.9'
   - version: '3.8.6'
-    isDefault: true
   - version: '3.9.1'
-  - version: 'anaconda3-5.2.0'
+  - version: '3.10.13'
+    isDefault: true
+  - version: '3.11.10'
+  - version: '3.12.7'
+  - version: 'anaconda3-2024.10.1'
+  - version: 'miniconda3-3.10-24.11.1-0'

applications/shell.yml

@@ -1,7 +1,7 @@
 name: shell
 shortName: sh
 summary: Shell Script
-defaultVersion: '4.2.46'
+defaultVersion: '5.1.8'
 versions:
-  - version: '4.2.46'
+  - version: '5.1.8'
     isDefault: true

assets/python/hello_world.pyi

@@ -13,8 +13,7 @@
 #                                                                  #
 # ---------------------------------------------------------------- #
 
-import pymatgen as mg
+import numpy as np
 
-si = mg.Element("Si")
-
-print(si.atomic_mass)
+pi_value = np.pi
+print(pi_value)

assets/python/ml/generation/README.md

@@ -2,7 +2,7 @@
 
 This directory contains the work corresponding to the PythonML implementation. Further documentation can be found here:
 
-https://docs.exabyte.io/software-directory/machine-learning/python-ml/overview/
+https://docs.mat3ra.com/software-directory/machine-learning/python-ml/overview/
 
 ## Current Status
 

assets/python/ml/requirements.j2.txt

@@ -1,6 +1,6 @@
 # ----------------------------------------------------------------- #
 #                                                                   #
-#  PythonML Package Requirements for use on the Exabyte.io Platform #
+#  Example Python package requirements for the Mat3ra platform      #
 #                                                                   #
 #  Will be used as follows:                                         #
 #                                                                   #
@@ -14,43 +14,10 @@
 #   - https://pip.pypa.io/en/stable/reference/pip_install           #
 #   - https://virtualenv.pypa.io/en/stable/                         #
 #                                                                   #
-#  The package set below is a stable working set of pymatgen and    #
-#  all of its dependencies.  Please adjust the list to include      #
-#  your preferred packages.                                         #
-#                                                                   #
 # ----------------------------------------------------------------- #
 
-# Python 3 packages
-certifi==2020.12.5
-chardet==4.0.0
-cycler==0.10.0
-decorator==4.4.2
-future==0.18.2
-idna==2.10
-kiwisolver==1.3.1
-matplotlib==3.3.4
-monty==4.0.2
-mpmath==1.2.1
-networkx==2.5
-numpy==1.19.5
-palettable==3.3.0
-pandas==1.1.5
-Pillow==8.1.0
-plotly==4.14.3
-pymatgen==2021.2.8.1
-pyparsing==2.4.7
-python-dateutil==2.8.1
-pytz==2021.1
-requests==2.25.1
-retrying==1.3.3
-ruamel.yaml==0.16.12
-ruamel.yaml.clib==0.2.2
-scikit-learn==0.24.1
-scipy==1.5.4
-six==1.15.0
-spglib==1.16.1
-sympy==1.7.1
-tabulate==0.8.7
-uncertainties==3.1.5
-urllib3==1.26.3
-xgboost==1.4.2;python_version>="3.6"
+matplotlib
+numpy
+scikit-learn
+xgboost
+pandas

assets/python/requirements.j2.txt

@@ -14,42 +14,9 @@
 #   - https://pip.pypa.io/en/stable/reference/pip_install           #
 #   - https://virtualenv.pypa.io/en/stable/                         #
 #                                                                   #
-#  The package set below is a stable working set of pymatgen and    #
-#  all of its dependencies.  Please adjust the list to include      #
-#  your preferred packages.                                         #
+#  Adjust the list to include your preferred packages.              #
 #                                                                   #
 # ----------------------------------------------------------------- #
 
-# Python 3 packages
-certifi==2020.12.5
-chardet==4.0.0
-cycler==0.10.0
-decorator==4.4.2
-future==0.18.2
-idna==2.10
-kiwisolver==1.3.1
-matplotlib==3.3.4
-monty==4.0.2
-mpmath==1.2.1
-networkx==2.5
-numpy==1.19.5
-palettable==3.3.0
-pandas==1.1.5
-Pillow==8.1.0
-plotly==4.14.3
-pymatgen==2021.2.8.1
-pyparsing==2.4.7
-python-dateutil==2.8.1
-pytz==2021.1
-requests==2.25.1
-retrying==1.3.3
-ruamel.yaml==0.16.12
-ruamel.yaml.clib==0.2.2
-scipy==1.5.4
-six==1.15.0
-spglib==1.16.1
-sympy==1.7.1
-tabulate==0.8.7
-uncertainties==3.1.5
-urllib3==1.26.3
-xgboost==1.4.2
+numpy<2
+

assets/shell/bash_job_espresso_pw_scf.j2.sh

@@ -15,7 +15,7 @@
 #    7. email about job abort, begin, end  (-m abe)                #
 #    8. email address to use               (-M)                    #
 #                                                                  #
-#  For more information visit https://docs.exabyte.io/cli/jobs     #
+#  For more information visit https://docs.mat3ra.com/cli/jobs     #
 # ---------------------------------------------------------------- #
 
 #PBS -N ESPRESSO-TEST
@@ -25,10 +25,10 @@
 #PBS -l walltime=00:00:10:00
 #PBS -q D
 #PBS -m abe
-#PBS -M info@exabyte.io
+#PBS -M info@mat3ra.com
 
 # load module
-module add espresso/540-i-174-impi-044
+module add espresso
 
 # go to the job working directory
 cd $PBS_O_WORKDIR