Develop

Dockerfile

@@ -0,0 +1,58 @@
+# Use Ubuntu base image and install Miniforge manually
+FROM ubuntu:22.04
+
+# Set working directory
+WORKDIR /workspace
+
+# Set environment variables
+ENV CONDA_ENV_NAME=my_atomgpt
+ENV PYTHONUNBUFFERED=1
+
+# Prevent interactive prompts during installation
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
+    git \
+    wget \
+    build-essential \
+    curl \
+    ca-certificates \
+    && rm -rf /var/lib/apt/lists/*
+
+# Download and install Miniforge
+RUN wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O miniforge.sh && \
+    bash miniforge.sh -b -p /opt/conda && \
+    rm miniforge.sh
+
+# Add conda to PATH
+ENV PATH="/opt/conda/bin:${PATH}"
+
+# Create conda environment with Python 3.10
+RUN conda create --name ${CONDA_ENV_NAME} python=3.10 -y
+
+# Make RUN commands use the conda environment
+SHELL ["conda", "run", "-n", "my_atomgpt", "/bin/bash", "-c"]
+
+# Clone AtomGPT repository
+RUN git clone https://github.com/atomgptlab/atomgpt.git && \
+    cd atomgpt && \
+    pip install -e .
+
+# Set the default working directory to atomgpt
+WORKDIR /workspace/atomgpt
+
+# Activate conda environment by default
+RUN echo "conda activate ${CONDA_ENV_NAME}" >> ~/.bashrc
+
+# Default command
+CMD ["/bin/bash"]
+
+
+###################################
+# Instructions
+#docker build -t atomgpt .
+#docker login
+#docker tag atomgpt atomgptlab/atomgpt:latest
+#docker push atomgptlab/atomgpt:latest
+#docker pull atomgptlab/atomgpt:latest

atomgpt/__init__.py

@@ -1,3 +1,3 @@
 """Version number."""
 
-__version__ = "2025.6.7"
+__version__ = "2025.9.7"

environment.yml

@@ -1,45 +1,47 @@
-name: atomgpt
+name: my_atomgpt
 channels:
   - conda-forge
 dependencies:
   - _libgcc_mutex=0.1=conda_forge
   - _openmp_mutex=4.5=2_gnu
-  - bzip2=1.0.8=h4bc722e_7
-  - ca-certificates=2025.4.26=hbd8a1cb_0
-  - ld_impl_linux-64=2.43=h712a8e2_4
-  - libexpat=2.7.0=h5888daf_0
+  - bzip2=1.0.8=hda65f42_8
+  - ca-certificates=2025.8.3=hbd8a1cb_0
+  - ld_impl_linux-64=2.44=ha97dd6f_2
+  - libexpat=2.7.1=hecca717_0
   - libffi=3.4.6=h2dba641_1
-  - libgcc=15.1.0=h767d61c_2
-  - libgcc-ng=15.1.0=h69a702a_2
-  - libgomp=15.1.0=h767d61c_2
-  - liblzma=5.8.1=hb9d3cd8_1
-  - libnsl=2.0.1=hd590300_0
-  - libsqlite=3.49.2=hee588c1_0
-  - libuuid=2.38.1=h0b41bf4_0
+  - libgcc=15.1.0=h767d61c_5
+  - libgcc-ng=15.1.0=h69a702a_5
+  - libgomp=15.1.0=h767d61c_5
+  - liblzma=5.8.1=hb9d3cd8_2
+  - libnsl=2.0.1=hb9d3cd8_1
+  - libsqlite=3.50.4=h0c1763c_0
+  - libuuid=2.41.2=he9a06e4_0
   - libxcrypt=4.4.36=hd590300_1
   - libzlib=1.3.1=hb9d3cd8_2
   - ncurses=6.5=h2d0b736_3
-  - openssl=3.5.0=h7b32b05_1
-  - pip=25.1.1=pyh8b19718_0
-  - python=3.10.17=hd6af730_0_cpython
+  - openssl=3.5.4=h26f9b46_0
+  - pip=25.2=pyh8b19718_0
+  - python=3.10.18=hd6af730_0_cpython
   - readline=8.2=h8c095d6_2
-  - setuptools=80.8.0=pyhff2d567_0
-  - tk=8.6.13=noxft_h4845f30_101
+  - setuptools=80.9.0=pyhff2d567_0
+  - tk=8.6.13=noxft_hd72426e_102
   - wheel=0.45.1=pyhd8ed1ab_1
   - pip:
       - accelerate==1.7.0
       - aiohappyeyeballs==2.6.1
       - aiohttp==3.11.18
       - aiosignal==1.3.2
+      - alembic==1.16.5
       - annotated-types==0.7.0
       - ase==3.25.0
       - async-timeout==5.0.1
       - attrs==25.3.0
-      - bitsandbytes==0.45.5
+      - bitsandbytes==0.48.1
       - black==25.1.0
       - certifi==2025.4.26
       - charset-normalizer==3.4.2
       - click==8.2.1
+      - colorlog==6.9.0
       - contourpy==1.3.2
       - cut-cross-entropy==25.1.1
       - cycler==0.12.1
@@ -52,6 +54,7 @@ dependencies:
       - frozenlist==1.6.0
       - fsspec==2025.3.0
       - gguf==0.16.3
+      - greenlet==3.2.4
       - hf-transfer==0.1.9
       - hf-xet==1.1.2
       - huggingface-hub==0.32.0
@@ -63,6 +66,7 @@ dependencies:
       - joblib==1.5.1
       - kiwisolver==1.4.8
       - lazy-loader==0.4
+      - mako==1.3.10
       - markdown-it-py==3.0.0
       - markupsafe==3.0.2
       - matplotlib==3.10.3
@@ -88,6 +92,7 @@ dependencies:
       - nvidia-nccl-cu12==2.26.2
       - nvidia-nvjitlink-cu12==12.6.85
       - nvidia-nvtx-cu12==12.6.77
+      - optuna==3.6.2
       - packaging==25.0
       - pandas==2.2.3
       - pathspec==0.12.1
@@ -118,6 +123,7 @@ dependencies:
       - shtab==1.7.2
       - six==1.17.0
       - spglib==2.6.0
+      - sqlalchemy==2.0.43
       - sympy==1.14.0
       - threadpoolctl==3.6.0
       - tifffile==2025.5.10

requirements.txt

@@ -2,15 +2,17 @@ accelerate==1.7.0
 aiohappyeyeballs==2.6.1
 aiohttp==3.11.18
 aiosignal==1.3.2
+alembic==1.16.5
 annotated-types==0.7.0
 ase==3.25.0
 async-timeout==5.0.1
 attrs==25.3.0
-bitsandbytes==0.45.5
+bitsandbytes==0.48.1
 black==25.1.0
 certifi==2025.4.26
 charset-normalizer==3.4.2
 click==8.2.1
+colorlog==6.9.0
 contourpy==1.3.2
 cut-cross-entropy==25.1.1
 cycler==0.12.1
@@ -23,6 +25,7 @@ fonttools==4.58.0
 frozenlist==1.6.0
 fsspec==2025.3.0
 gguf==0.16.3
+greenlet==3.2.4
 hf-xet==1.1.2
 hf_transfer==0.1.9
 huggingface-hub==0.32.0
@@ -34,6 +37,7 @@ Jinja2==3.1.6
 joblib==1.5.1
 kiwisolver==1.4.8
 lazy_loader==0.4
+Mako==1.3.10
 markdown-it-py==3.0.0
 MarkupSafe==3.0.2
 matplotlib==3.10.3
@@ -59,7 +63,7 @@ nvidia-cusparselt-cu12==0.6.3
 nvidia-nccl-cu12==2.26.2
 nvidia-nvjitlink-cu12==12.6.85
 nvidia-nvtx-cu12==12.6.77
-optuna>=3.5,<4
+optuna==3.6.2
 packaging==25.0
 pandas==2.2.3
 pathspec==0.12.1
@@ -90,6 +94,7 @@ sentencepiece==0.2.0
 shtab==1.7.2
 six==1.17.0
 spglib==2.6.0
+SQLAlchemy==2.0.43
 sympy==1.14.0
 threadpoolctl==3.6.0
 tifffile==2025.5.10

setup.py

@@ -8,7 +8,7 @@
 
 setuptools.setup(
     name="atomgpt",
-    version="2025.6.7",
+    version="2025.9.7",
     author="Kamal Choudhary",
     author_email="kamal.choudhary@nist.gov",
     description="atomgpt",