paddle 1.1.5__tar.gz → 1.1.7__tar.gz

{paddle-1.1.5 → paddle-1.1.7}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.5
+current_version = 1.1.7
 commit = True
 tag = True
 

{paddle-1.1.5 → paddle-1.1.7}/.github/workflows/ci.yml

@@ -44,7 +44,8 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: [ubuntu-latest, macOS-latest]
+        #os: [ubuntu-latest, macOS-latest]
+        os: [ubuntu-latest]
     steps:
       - name: Check out code
         uses: actions/checkout@v4

{paddle-1.1.5 → paddle-1.1.7}/.gitignore

@@ -205,3 +205,6 @@ cython_debug/
 marimo/_static/
 marimo/_lsp/
 __marimo__/
+
+# docker
+docker-compose.override.yaml

{paddle-1.1.5 → paddle-1.1.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: paddle
-Version: 1.1.5
+Version: 1.1.7
 Summary: Python Atmospheric Dynamics: Discovery and Learning about Exoplanets. An open-source, user-friendly python frontend of canoe
 Project-URL: Homepage, https://github.com/elijah-mullens/paddle
 Project-URL: Repository, https://github.com/elijah-mullens/paddle
@@ -23,7 +23,8 @@ Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.9
 Requires-Dist: kintera>=1.1.5
-Requires-Dist: snapy>=0.8.2
+Requires-Dist: scipy
+Requires-Dist: snapy>=0.8.1
 Requires-Dist: torch<=2.7.1,>=2.7.0
 Provides-Extra: dev
 Requires-Dist: pytest>=7; extra == 'dev'
@@ -33,43 +34,66 @@ Description-Content-Type: text/markdown
 Python Atmospheric Dynamics: Discovering and Learning about Exoplanets. An open-source, user-friendly python version of canoe.
 
 ## Install docker and docker-compose plugin
+1. install docker with compose
+```bash
+curl -fsSL https://get.docker.com | sudo sh
+```
 
+1. start docker
+sudo systemctl start docker
 
-## Create a python virtual environment
+## Test package
+1. Create a python virtual environment
 ```bash
 python -m venv pyenv
 ```
 
-# Create a docker container
+2. Install paddle package
+```bash
+pip install paddle
+```
+
+3. Run test
+```bash
+cd tests
+python test_saturn_adiabat.py
+```
+
+## Docker user guide
+
+2. Create a docker container
 ```bash
 make up
 ```
 
-# Terminate a docker container
+3. Terminate a docker container
 ```bash
 make down
 ```
 
-# Start a docker container
+4. Start a docker container
 ```bash
 make start
 ```
 
-# Build a new docker image (rarely used)
+5. Build a new docker image (rarely used)
 ```bash
 make build
 ```
 
-## For Development
+## For Developer
+
+### Clone repository
+```bash
+https://github.com/elijah-mullens/paddle
+```
+
 ### Cache your github credential
 ```bash
 git config credential.helper 'cache --timeout=86400'
 ```
 
 ### Install paddle package
-```bash
-pip install paddle
-```
 
 ### Install pre-commit hook
 ```bash
@@ -80,3 +104,7 @@ pip install pre-commit
 ```bash
 pre-commit install
 ```
+
+## Troubleshooting
+1. If you do not have docker compose
+Remove your current docker installation, it could be docker or docker.io

paddle-1.1.7/README.md

@@ -0,0 +1,78 @@
+# paddle
+Python Atmospheric Dynamics: Discovering and Learning about Exoplanets. An open-source, user-friendly python version of canoe.
+
+## Install docker and docker-compose plugin
+1. install docker with compose
+```bash
+curl -fsSL https://get.docker.com | sudo sh
+```
+
+1. start docker
+sudo systemctl start docker
+
+## Test package
+1. Create a python virtual environment
+```bash
+python -m venv pyenv
+```
+
+2. Install paddle package
+```bash
+pip install paddle
+```
+
+3. Run test
+```bash
+cd tests
+python test_saturn_adiabat.py
+```
+
+## Docker user guide
+
+2. Create a docker container
+```bash
+make up
+```
+
+3. Terminate a docker container
+```bash
+make down
+```
+
+4. Start a docker container
+```bash
+make start
+```
+
+5. Build a new docker image (rarely used)
+```bash
+make build
+```
+
+## For Developer
+
+### Clone repository
+```bash
+https://github.com/elijah-mullens/paddle
+```
+
+### Cache your github credential
+```bash
+git config credential.helper 'cache --timeout=86400'
+```
+
+### Install paddle package
+
+### Install pre-commit hook
+```bash
+pip install pre-commit
+```
+
+### Install pre-commit hook
+```bash
+pre-commit install
+```
+
+## Troubleshooting
+1. If you do not have docker compose
+Remove your current docker installation, it could be docker or docker.io

paddle-1.1.7/docker/Dockerfile

@@ -0,0 +1,131 @@
+# syntax=docker/dockerfile:1.7
+ARG CUDA_VER=12.9.1
+ARG UBUNTU_VER=22.04
+
+############################
+# Base CUDA toolchain
+############################
+FROM ubuntu:${UBUNTU_VER} AS base
+
+ENV DEBIAN_FRONTEND=noninteractive \
+    TZ=UTC
+
+# System deps (C++ toolchain, Python, venv, git, neovim, etc.)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+      gosu tini \
+      build-essential \
+      gcc g++ gfortran \
+      ninja-build \
+      cmake \
+      git curl ca-certificates \
+      python3 python3-pip python3-venv python3-dev \
+      pkg-config \
+      libssl-dev \
+      ripgrep fd-find unzip neovim \
+      clangd \
+      nodejs npm \
+      && rm -rf /var/lib/apt/lists/*
+
+# Make fd available as `fd` (Ubuntu calls it fdfind)
+RUN update-alternatives --install /usr/bin/fd fd /usr/bin/fdfind 50
+
+# Default editor env
+ENV EDITOR=nvim VISUAL=nvim
+
+# System-wide git editor default (users can override)
+RUN git config --system core.editor "nvim"
+
+# Pre-warm plugins (optional, speeds first start)
+# This runs Neovim headless to install plugins via lazy.nvim.
+RUN nvim --headless "+Lazy! sync" +qa || true
+
+############################
+# Convenient command-line tools
+############################
+
+# ---- after base tooling is installed, before switching USER ----
+# Create a tools dir and put it on PATH
+RUN mkdir -p /opt/tools
+ENV PATH="/opt/tools:${PATH}"
+
+# Copy all helper scripts
+COPY docker/scripts/ /opt/tools/
+# Ensure executables
+RUN find /opt/tools -type f -name "*.sh" -exec chmod +x {} \; \
+    && for f in /opt/tools/*.sh; do ln -sf "$f" "/usr/local/bin/$(basename "${f%.sh}")"; done
+# The symlink makes command-line tools available (no .sh needed)
+
+############################
+# Configure non-root user and Python venv
+############################
+
+# Python venv in /opt/venv (global, fast, easy)
+RUN python3 -m venv /opt/venv
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH="/opt/venv/bin:${PATH}"
+
+# Upgrade pip/setuptools/wheel early
+RUN pip install --upgrade pip setuptools wheel build
+
+# Optional: pin pip resolver behavior and set default index/extra-index if needed
+# COPY docker/pip.conf /etc/pip.conf
+
+# Put a base Neovim config in /etc/skel so future users get it,
+# and also install for the existing dev user.
+#RUN mkdir -p /etc/skel/.config/nvim
+#COPY docker/nvim/ /etc/skel/.config/nvim/
+#RUN mkdir -p /home/${USERNAME}/.config/nvim && \
+#    cp -r /etc/skel/.config/nvim/* /home/${USERNAME}/.config/nvim/ && \
+#    chown -R ${USERNAME}:${USERNAME} /home/${USERNAME}/.config/nvim
+
+############################
+# Cache Python wheels separately (optional but recommended)
+############################
+FROM base AS wheels
+WORKDIR /tmp/wheels
+# If you use requirements.txt:
+COPY docker/requirements.txt .
+RUN --mount=type=cache,target=/root/.cache/pip \
+    pip wheel -r requirements.txt -w /tmp/wheelhouse
+
+# If you use Poetry/pyproject, replace the above with:
+# COPY pyproject.toml poetry.lock ./
+# RUN pip install "poetry>=1.8.0"
+# RUN --mount=type=cache,target=/root/.cache/pip poetry export -f requirements.txt --without-hashes | tee req.txt
+# RUN --mount=type=cache,target=/root/.cache/pip pip wheel -r req.txt -w /tmp/wheelhouse
+
+############################
+# Dev image
+############################
+FROM base AS dev
+WORKDIR /workspace
+
+# Load for login shells
+#RUN printf 'alias vi=nvim\nalias vim=nvim\nexport TERM=xterm-256color\n' >> /home/${USERNAME}/.bashrc
+
+# Bring in prebuilt wheels (fast installs)
+COPY --from=wheels /tmp/wheelhouse /tmp/wheelhouse
+COPY docker/requirements.txt /workspace/docker/requirements.txt
+
+# Install Python deps from wheels first, then fall back to index
+RUN --mount=type=cache,target=/root/.cache/pip \
+    pip install --no-index --find-links=/tmp/wheelhouse -r /workspace/docker/requirements.txt \
+ || pip install -r /workspace/docker/requirements.txt
+
+# (Optional) CUDA env defaults for many toolchains
+ENV TORCH_CUDA_ARCH_LIST="8.6;8.9;9.0+PTX"  \
+    CUDA_CACHE_MAXSIZE=2147483647
+
+# Put your entrypoint in place
+COPY docker/entrypoint.sh /usr/local/bin/entrypoint.sh
+RUN chmod +x /usr/local/bin/entrypoint.sh
+
+# Keep the workspace owned by the non-root user
+#RUN chown -R ${USERNAME}:${USERNAME} /workspace
+#USER ${USERNAME}
+
+#ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
+#CMD ["/bin/bash"]
+
+ENTRYPOINT ["/usr/bin/tini","--","/usr/local/bin/entrypoint.sh"]
+CMD ["/bin/bash"]

paddle-1.1.7/docker/requirements.txt

@@ -0,0 +1,2 @@
+numpy
+scipy

paddle-1.1.7/docker-compose.override.yaml.tmp

@@ -0,0 +1,17 @@
+services:
+  dev:
+    build:
+      dockerfile: docker/Dockerfile.cuda
+      args:
+        CUDA_VER: "12.9.1"
+    deploy:
+      resources:
+        reservations:
+          devices:
+            # Activate this if your system supports GPU
+            - capabilities: [gpu]
+    volumes:
+      # This is your main working directory
+      - ${HOME}/work:/work
+      # This is where you put your large simulation data
+      - ${HOME}/data/:/data

paddle-1.1.7/docker-compose.yaml

@@ -0,0 +1,20 @@
+services:
+  dev:
+    image: paddle
+    build:
+      context: .
+      dockerfile: docker/Dockerfile
+      args:
+        CUDA_VER: "12.9.1"
+        UBUNTU_VER: "22.04"
+    environment:
+      - USERNAME=${USER}
+      - USER_UID=${USER_UID}
+      - USER_GID=${USER_GID}
+    # This is volatile
+    # Make sure that you use override.yaml for permanent changes
+    working_dir: /work
+    tty: true
+    stdin_open: true
+    ports:
+      - "8888:8888"

{paddle-1.1.5 → paddle-1.1.7}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "paddle"
-version = "1.1.5"
+version = "1.1.7"
 description = "Python Atmospheric Dynamics: Discovery and Learning about Exoplanets. An open-source, user-friendly python frontend of canoe"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -33,7 +33,8 @@ classifiers = [
 dependencies = [
   "torch>=2.7.0,<=2.7.1",
   "kintera>=1.1.5",
-  "snapy>=0.8.2",
+  "snapy>=0.8.1",
+  "scipy"
 ]
 
 [project.optional-dependencies]

{paddle-1.1.5 → paddle-1.1.7}/src/paddle/__init__.py

@@ -4,4 +4,4 @@ from .find_init_params import find_init_params
 from .evolve_kinetics import evolve_kinetics
 
 __all__ = ["setup_profile", "write_profile", "find_init_params", "evolve_kinetics"]
-__version__ = "1.1.5"
+__version__ = "1.1.7"

paddle-1.1.5/README.md

@@ -1,51 +0,0 @@
-# paddle
-Python Atmospheric Dynamics: Discovering and Learning about Exoplanets. An open-source, user-friendly python version of canoe.
-
-## Install docker and docker-compose plugin
-
-
-## Create a python virtual environment
-```bash
-python -m venv pyenv
-```
-
-# Create a docker container
-```bash
-make up
-```
-
-# Terminate a docker container
-```bash
-make down
-```
-
-# Start a docker container
-```bash
-make start
-```
-
-# Build a new docker image (rarely used)
-```bash
-make build
-```
-
-## For Development
-### Cache your github credential
-```bash
-git config credential.helper 'cache --timeout=86400'
-```
-
-### Install paddle package
-```bash
-pip install paddle
-```
-
-### Install pre-commit hook
-```bash
-pip install pre-commit
-```
-
-### Install pre-commit hook
-```bash
-pre-commit install
-```

paddle-1.1.5/docker-compose.yaml

@@ -1,29 +0,0 @@
-services:
-  dev:
-    image: paddle
-    build:
-      context: .
-      dockerfile: docker/Dockerfile
-      args:
-        CUDA_VER: "12.9.1"
-        UBUNTU_VER: "22.04"
-    environment:
-      - USERNAME=${USER}
-      - USER_UID=${USER_UID}
-      - USER_GID=${USER_GID}
-    deploy:
-      resources:
-        reservations:
-          devices:
-            # If your system does not have gpu, remove it from the []
-            - capabilities: [gpu]
-    volumes:
-      # This is your main working directory
-      - ${HOME}/projects:/projects
-      # This is where you put your large simulation data
-      - ${HOME}/data/:/data
-    working_dir: /projects
-    tty: true
-    stdin_open: true
-    ports:
-      - "8888:8888"