Initial commit combining various codes into one repo

Author: muhrin

.github/workflows/tests.yaml

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+name: Dynamic Submodule Test Runner
+
+on:
+   push:
+      branches:
+         - develop
+
+jobs:
+   # 1. SETUP JOB: Installs all dependencies and caches the environment
+   setup_env:
+      runs-on: ubuntu-latest
+      outputs:
+         # We no longer use this conditional output directly, but keep it for structure
+         env_ready: true
+
+      steps:
+         -  name: Checkout Code and Submodules
+            uses: actions/checkout@v4
+            with:
+               submodules: true
+               token: ${{ secrets.CAMML_READ_TOKEN }}
+
+         -  name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+               python-version: '3.13'
+
+         -  name: Generate Submodule Hash Key
+            id: submodule_key_gen
+            run: |
+               SUBMODULE_HASHES=$(git submodule status \
+                   | sed 's/^[ +-]//' \
+                   | awk '{print $1}' \
+                   | tr '\n' '_')  
+               echo "key=$SUBMODULE_HASHES" >> $GITHUB_OUTPUT
+
+         -  name: Cache Python dependencies
+            uses: actions/cache@v4
+            id: cache-venv
+            with:
+               path: |
+                  ${{ env.pythonLocation }}/lib/python*/site-packages
+                  ${{ env.pythonLocation }}/bin
+               # Key construction is crucial for consistency
+               key: ${{ runner.os }}-python-3.13-${{ steps.submodule_key_gen.outputs.key }}
+
+         -  name: Install All Submodules (If cache miss)
+            # Conditional logic now works correctly
+            if: steps.cache-venv.outputs.cache-hit != 'true'
+            run: |
+               echo "Installing ALL interdependent codes..."
+               pip install -e "./reax[dev]" -e "./tensorial[dev]" -e "./e3md[dev]" -e "./e3response[dev]" -e "./e3gen[dev]"
+
+   # 2. TEST JOB: Runs tests in parallel using the cached environment
+   test_submodules:
+      runs-on: ubuntu-latest
+      needs: setup_env
+
+      strategy:
+         fail-fast: false          # ✅ Disable stopping early
+         matrix:
+            submodule_path: [ reax, tensorial, e3md, e3response, e3gen ]
+
+      steps:
+         -  name: Checkout Code (Minimal checkout for file access)
+            uses: actions/checkout@v4
+            with:
+               submodules: true
+               token: ${{ secrets.CAMML_READ_TOKEN }}
+
+         -  name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+               python-version: '3.13'
+
+         -  name: Generate Submodule Hash Key for Restore
+            id: submodule_key_restore
+            run: |
+               SUBMODULE_HASHES=$(git submodule status \
+                   | sed 's/^[ +-]//' \
+                   | awk '{print $1}' \
+                   | tr '\n' '_')  
+               echo "key=$SUBMODULE_HASHES" >> $GITHUB_OUTPUT
+
+         -  name: Restore Cached Dependencies
+            uses: actions/cache@v4
+            with:
+               path: |
+                  ${{ env.pythonLocation }}/lib/python*/site-packages
+                  ${{ env.pythonLocation }}/bin
+               key: ${{ runner.os }}-python-3.13-${{ steps.submodule_key_restore.outputs.key }}
+
+         -  name: Run Test for ${{ matrix.submodule_path }}
+            run: |
+               echo "Running tests for ${{ matrix.submodule_path }}..."
+               pytest ./${{ matrix.submodule_path }}/test

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.pytest_cache
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+#Ipython Notebook
+.ipynb_checkpoints
+
+
+# JetBrains IDE stuff
+.idea/
+
+# Virtual environment directories
+/venv*/
+
+.benchmarks
+
+examples/*/
+
+.vscode/
+
+local/
+
+# DOCS
+docs/build/
+docs/source/starting/data/

.gitmodules

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+[submodule "reax"]
+	path = reax
+	url = https://github.com/camml-lab/reax.git
+	branch = develop
+[submodule "tensorial"]
+	path = tensorial
+	url = https://github.com/camml-lab/tensorial.git
+	branch = develop
+[submodule "e3md"]
+	path = e3md
+	url = https://github.com/camml-lab/e3md.git
+	branch = develop
+[submodule "e3response"]
+	path = e3response
+	url = https://github.com/camml-lab/e3response.git
+	branch = develop
+[submodule "e3gen"]
+	path = e3gen
+	url = https://github.com/camml-lab/e3gen.git
+	branch = develop
+

README.md

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+# Welcome to CAMML codes
+
+[![Build Status](https://github.com/camml-lab/camml-codes/actions/workflows/tests.yaml/badge.svg)](https://github.com/camml-lab/camml-codes/actions)
+
+This is our repository that groups together the various codes developed in the CAMML group.
+
+## Users
+
+## Developers
+
+This repo uses [git submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules) the track various codes which each
+live in their own repository. We do this using their `https://` versions which means you are asked for your credentials
+every time you want to access them.
+To avoid this you can run the following command which will use your git credentials instead:
+
+```bash
+# Run this command once to tell Git: 
+# "Any time you see an HTTPS URL for github.com, use the SSH URL instead."
+git config --global url."git@github.com:".insteadOf "https://github.com/"
+```

e3gen

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+#!/bin/bash
+
+# Ensure Git submodule configuration is initialized
+git submodule init
+
+# Loop through all submodules defined in .gitmodules
+# This command reads the submodule paths
+git config -f .gitmodules --get-regexp submodule\..*\.path | while read key path
+do
+    echo "--- Attempting to update $path ---"
+
+    # Attempt to update/clone the submodule using a selective command
+    # The '|| true' ensures the entire script does not exit on failure
+    if git submodule update --init -- $path; then
+        echo "Successfully checked out $path."
+
+        # Install in editable mode if it's a valid package directory
+        if [ -d "$path" ] && [ -f "$path/setup.py" ]; then
+            echo "Installing $path in editable mode (pip install -e)."
+            pip install -e "$path"
+        fi
+    else
+        # Handle Permission Failure (Non-fatal warning)
+        echo "🚨 WARNING: Failed to update/clone $path due to access issues."
+        echo "Skipping installation for this module. You can still use available codes."
+    fi
+    echo "-----------------------------------"
+done
+
+echo "Setup complete! Environment includes all accessible codes."