paddle 1.1.10__tar.gz → 1.1.14__tar.gz

{paddle-1.1.10 → paddle-1.1.14}/.bumpversion.cfg

@@ -1,9 +1,9 @@
 [bumpversion]
-current_version = 1.1.10
+current_version = 1.1.14
 commit = True
 tag = True
 
-[bumpversion:file:src/paddle/__init__.py]
+[bumpversion:file:paddle/__init__.py]
 search = __version__ = "{current_version}"
 replace = __version__ = "{new_version}"
 

paddle-1.1.10/.github/workflows/bump-and-tag.yaml → paddle-1.1.14/.github/workflows/cd.yml

@@ -1,4 +1,4 @@
-name: Bump Version and Tag
+name: Release to PyPI
 
 on:
   pull_request:
@@ -9,41 +9,74 @@ env:
   PYTHON_VERSION: "3.11"
 
 jobs:
-  bump-version:
+  release:
+    if: github.event.pull_request.merged == true
     runs-on: ubuntu-latest
     permissions:
-      contents: write
-      pull-requests: write
+      contents: write # push commits/tags, create release
+      pull-requests: write # comment on PR
+      id-token: write # needed by PyPI OIDC if you switch to OIDC auth
 
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
         with:
-          fetch-depth: 0
+          fetch-depth: 0 # need full history for bumpversion/tags
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: ${{ env.PYTHON_VERSION }}
+          cache: pip
 
       - name: Configure Git
         run: |
           git config user.name "github-actions[bot]"
           git config user.email "github-actions[bot]@users.noreply.github.com"
 
-      - name: Bump version and push tag
+      # 🔹 Bump version & create tag (same as before)
+      - name: Bump version and create tag
         id: bump_version
         uses: jasonamyers/github-bumpversion-action@v1.0.5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+      # 🔹 Push the bump commit and tag back to main
       - name: Push changes
         uses: ad-m/github-push-action@master
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          branch: ${{ github.ref }}
+          branch: ${{ github.base_ref }}
           tags: true
 
+      # 🔹 Build distribution artifacts
+      - name: Build sdist and wheel
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+          python -m build
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/*
+
+      # 🔹 Publish to PyPI
+      - name: Download wheels
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          verbose: true
+
+      # 🔹 Generate Release Notes
       - name: Generate Release Notes
         uses: octokit/request-action@v2.x
         id: get_release_notes
@@ -53,6 +86,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+      # 🔹 Create GitHub Release
       - name: Create GitHub release
         id: create_release
         uses: actions/create-release@v1.1.4
@@ -65,6 +99,7 @@ jobs:
           prerelease: false
           body: ${{ fromJson(steps.get_release_notes.outputs.data).body }}
 
+      # 🔹 Comment on the PR with release notes
       - name: Post comment on PR with release notes
         uses: actions/github-script@v7
         with:
@@ -74,5 +109,5 @@ jobs:
               issue_number: context.payload.pull_request.number,
               owner: context.repo.owner,
               repo: context.repo.repo,
-              body: `🎉 Released v${{ steps.bump_version.outputs.new_ver }}!\n\n${notes}`
+              body: `🎉 Released v${{ steps.bump_version.outputs.new_ver }} to PyPI!\n\n${notes}`
             })

{paddle-1.1.10 → paddle-1.1.14}/.gitignore

@@ -214,3 +214,7 @@ docker-compose.override.yaml
 
 # restart outputs
 *.restart
+
+# python environment
+.env
+.pyenv

paddle-1.1.14/Makefile

@@ -0,0 +1,61 @@
+ENV_FILE := .env
+UID := $$(id -u)
+GID := $$(id -g)
+GITCONFIG := $${HOME}/.gitconfig
+GITCREDENTIALS := $${HOME}/.git-credentials
+
+.PHONY: help env up down ps start build
+
+# Show help for each target
+help: ## Show this help message
+	@echo "Available commands:"
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | \
+		awk 'BEGIN {FS = ":.*?## "}; {printf "  \033[36m%-12s\033[0m %s\n", $$1, $$2}'
+
+env: ## Generate the .env file with git configs first, then user info
+	@# Check if either variable is missing
+	@if ! grep -q '^GITCONFIG=' $(ENV_FILE) 2>/dev/null || \
+	    ! grep -q '^GITCREDENTIALS=' $(ENV_FILE) 2>/dev/null; then \
+		if [ -f "$${HOME}/.gitconfig" ]; then \
+			echo "GITCONFIG=$${HOME}/.gitconfig" > $(ENV_FILE); \
+		else \
+			touch "$${HOME}/.gitconfig"; \
+			echo "GITCONFIG=$${HOME}/.gitconfig" > $(ENV_FILE); \
+		fi; \
+		if [ -f "$${HOME}/.git-credentials" ]; then \
+			echo "GITCREDENTIALS=$${HOME}/.git-credentials" >> $(ENV_FILE); \
+		else \
+			touch "$${HOME}/.git-credentials"; \
+			echo "[credential]" >> "$${HOME}/.gitconfig"; \
+			echo "    helper = store" >> "$${HOME}/.gitconfig"; \
+			echo "GITCREDENTIALS=$${HOME}/.git-credentials" >> $(ENV_FILE); \
+		fi; \
+		echo "USER=$$(id -un)"    >> $(ENV_FILE); \
+		echo "USER_UID=$$(id -u)" >> $(ENV_FILE); \
+		echo "USER_GID=$$(id -g)" >> $(ENV_FILE); \
+		echo "Created $(ENV_FILE):"; cat $(ENV_FILE); \
+	fi
+
+up: env ## Start docker containers in the background
+	@docker compose up -d
+	@docker compose exec dev bash -c '\
+		USER_HOME=$$(eval echo ~$$USERNAME); \
+		if [ -f /etc/git-credentials ] && [ ! -f $$USER_HOME/.git-credentials ]; then \
+			cp /etc/git-credentials $$USER_HOME/.git-credentials; \
+			chown $${USER_UID}:$${USER_GID} $$USER_HOME/.git-credentials; \
+			git config --global credential.helper store; \
+		fi \
+	'
+
+down: env ## Stop and remove docker containers
+	@docker compose down
+
+ps: env ## Show container status
+	@docker compose ps
+
+start: env ## Open a bash shell inside the 'dev' container as the host user, exit without error
+	@docker compose exec --user $(UID):$(GID) dev \
+		bash -c 'git config --global --add safe.directory /paddle; exec bash'
+
+build: env ## Build (or rebuild) the 'dev' container and start it
+	@docker compose up -d --build dev

{paddle-1.1.10 → paddle-1.1.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: paddle
-Version: 1.1.10
+Version: 1.1.14
 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
@@ -93,6 +93,11 @@ https://github.com/elijah-mullens/paddle
 git config credential.helper 'cache --timeout=86400'
 ```
 
+### Create a python virtual environment
+```bash
+python -m venv .pyenv
+```
+
 ### Install paddle package
 
 ### Install pre-commit hook

{paddle-1.1.10 → paddle-1.1.14}/README.md

@@ -61,6 +61,11 @@ https://github.com/elijah-mullens/paddle
 git config credential.helper 'cache --timeout=86400'
 ```
 
+### Create a python virtual environment
+```bash
+python -m venv .pyenv
+```
+
 ### Install paddle package
 
 ### Install pre-commit hook

{paddle-1.1.10 → paddle-1.1.14}/docker/Dockerfile

@@ -24,6 +24,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
       ripgrep fd-find unzip neovim \
       clangd \
       nodejs npm \
+      libnetcdf-dev nco ncview \
       && rm -rf /var/lib/apt/lists/*
 
 # Make fd available as `fd` (Ubuntu calls it fdfind)

{paddle-1.1.10 → paddle-1.1.14}/docker/entrypoint.sh

@@ -34,16 +34,6 @@ done
 echo 'export EDITOR=nvim; export VISUAL=nvim' >> "${HOME_DIR}/.bashrc" || true
 chown "${USER_UID}:${USER_GID}" "${HOME_DIR}/.bashrc" || true
 
-# Configure git
-if [ -f /host/.gitconfig ] && [ ! -e "${HOME_DIR}/.gitconfig" ]; then
-  ln -s /host/.gitconfig "${HOME_DIR}/.gitconfig"
-  chown -h "${USER_UID}:${USER_GID}" "${HOME_DIR}/.gitconfig" || true
-
-  #cp /host/.gitconfig "${HOME_DIR}/.gitconfig"
-  #chown "${USER_UID}:${USER_GID}" "${HOME_DIR}/.gitconfig"
-  #chmod 600 "${HOME_DIR}/.gitconfig"
-fi
-
 # Drop privileges (use tini/gosu if installed; otherwise su-exec/ runuser)
 if command -v gosu >/dev/null 2>&1; then
   exec gosu "${USER_UID}:${USER_GID}" "$@"

paddle-1.1.14/docker-compose.override.yaml.tmp

@@ -0,0 +1,26 @@
+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 maps your physical locations to locations in docker
+      # (lhs:rhs, lhs = workspace on physical machine : rhs = workspace on virtual machine)
+      # Here we set up two directorys: your docker workspace directory that stores paddle
+      # (all py scripts and notebooks)
+      # And your data directory, that stores large data products ('results')
+      # While this data directory won't always be used
+      # (you can optionally have smaller outputs stored locally in the workspace directory)
+      # It is useful for very large data products, like those of gcm or mcmc scripts.
+      - path_to_physical_directory/paddle_docker_workspace:/paddle_docker_workspace
+      - path_to_physical_data_directory/:/paddke_docker_data_storage
+
+    # This is your main workspace where you can modify your source code
+    working_dir: /paddle_docker_workspace

{paddle-1.1.10 → paddle-1.1.14}/docker-compose.yaml

@@ -11,9 +11,11 @@ services:
       - 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: /paddle_docker_workspace
+    volumes:
+      - .:/paddle
+      - ${GITCONFIG}:/etc/gitconfig
+      - ${GITCREDENTIALS}:/etc/git-credentials
+    working_dir: /paddle
     tty: true
     stdin_open: true
     ports:

paddle-1.1.14/docs/content/notebooks/Tutorial-1-SaturnAdiabat.ipynb

@@ -0,0 +1,19 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "17fa4485",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{paddle-1.1.10/tests → paddle-1.1.14/example_py_scripts}/robert.py

@@ -73,13 +73,12 @@ w[kIDN] = w[kIPR] / (Rd * temp)
 
 block_vars = {}
 block_vars["hydro_w"] = w
-block_vars = block.initialize(block_vars)
+block_vars, current_time = block.initialize(block_vars)
 
 block.set_user_output_func(call_user_output)
 
 # integration
 start_time = time.time()
-current_time = 0.0
 block.make_outputs(block_vars, current_time)
 
 while not block.intg.stop(block.inc_cycle(), current_time):
@@ -99,4 +98,3 @@ while not block.intg.stop(block.inc_cycle(), current_time):
     block.make_outputs(block_vars, current_time)
 
 block.finalize(block_vars, current_time)
-print("elapsed time = ", time.time() - start_time)

{paddle-1.1.10/tests → paddle-1.1.14/example_py_scripts}/robert.yaml

@@ -12,6 +12,13 @@ geometry:
   bounds: {x1min: 0., x1max: 1.5e3, x2min: 0., x2max: 1.e3, x3min: -0.5, x3max: 0.5}
   cells: {nx1: 300, nx2: 200, nx3: 1, nghost: 3}
 
+distribute:
+  backend: gloo
+  layout: slab
+  nb2: 4
+  nb3: 1
+  verbose: false
+
 dynamics:
   equation-of-state:
     type: ideal-gas
@@ -24,8 +31,8 @@ dynamics:
     pressure-margin: 1.e-6
 
   reconstruct:
-    vertical: {type: weno5, scale: false, shock: true}
-    horizontal: {type: weno5, scale: false, shock: true}
+    vertical: {type: weno5, scale: false, shock: false}
+    horizontal: {type: weno5, scale: false, shock: false}
 
   riemann-solver:
     type: lmars

{paddle-1.1.10/tests → paddle-1.1.14/example_py_scripts}/shock.py

@@ -42,7 +42,7 @@ solid = torch.where(r1 < 0.1, 1, 0).to(torch.bool)
 block_vars = {}
 block_vars["hydro_w"] = w
 block_vars["solid"] = solid
-block_vars = block.initialize(block_vars)
+block_vars, current_time = block.initialize(block_vars)
 
 # integration
 current_time = 0.0

{paddle-1.1.10/tests → paddle-1.1.14/example_py_scripts}/straka.py

@@ -72,13 +72,12 @@ w[kIDN] = w[kIPR] / (Rd * temp)
 
 block_vars = {}
 block_vars["hydro_w"] = w
-block_vars = block.initialize(block_vars)
+block_vars, current_time = block.initialize(block_vars)
 
 block.set_user_output_func(call_user_output)
 
 # integration
 start_time = time.time()
-current_time = 0.0
 block.make_outputs(block_vars, current_time)
 
 while not block.intg.stop(block.inc_cycle(), current_time):
@@ -98,4 +97,3 @@ while not block.intg.stop(block.inc_cycle(), current_time):
     block.make_outputs(block_vars, current_time)
 
 block.finalize(block_vars, current_time)
-print("elapsed time = ", time.time() - start_time)

{paddle-1.1.10/tests → paddle-1.1.14/example_py_scripts}/straka.yaml

@@ -12,6 +12,13 @@ geometry:
   bounds: {x1min: 0., x1max: 6.4e3, x2min: 0., x2max: 25.6e3, x3min: 0., x3max: 25.6e3}
   cells: {nx1: 64, nx2: 256, nx3: 1, nghost: 3}
 
+distribute:
+  backend: gloo
+  layout: slab
+  nb2: 1
+  nb3: 1
+  verbose: false
+
 dynamics:
   equation-of-state:
     type: ideal-gas

{paddle-1.1.10/src → paddle-1.1.14}/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__ = "1.1.10"
+__version__ = "1.1.14"

{paddle-1.1.10 → paddle-1.1.14}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "paddle"
-version = "1.1.10"
+version = "1.1.14"
 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"

paddle-1.1.10/.github/workflows/cd.yml

@@ -1,55 +0,0 @@
-name: Deploy to PyPI
-
-on:
-  push:
-    branches: [main]
-    tags: [v*]
-
-jobs:
-  build:
-    name: Build distribution artifacts
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Setup Host Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-          cache: pip
-
-      - name: Install build backend
-        run: |
-          python -m pip install --upgrade pip
-          pip install build
-
-      - name: Build sdist and wheel
-        run: python -m build
-
-      - name: Upload artifacts
-        uses: actions/upload-artifact@v4
-        with:
-          name: dist
-          path: dist/*
-
-  publish-pypi:
-    name: Publish to PyPI
-    needs: build
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
-      contents: read
-    steps:
-      - name: Download wheels
-        uses: actions/download-artifact@v4
-        with:
-          name: dist
-          path: dist
-
-      - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
-          verbose: true

paddle-1.1.10/Makefile

@@ -1,26 +0,0 @@
-ENV_FILE := .env
-UID := $$(id -u)
-GID := $$(id -g)
-
-.PHONY: env up down build
-
-env:
-	@echo "USER=$$(id -un)" > $(ENV_FILE)
-	@echo "USER_UID=$$(id -u)" >> $(ENV_FILE)
-	@echo "USER_GID=$$(id -g)" >> $(ENV_FILE)
-	@echo "Wrote $(ENV_FILE):"; cat $(ENV_FILE)
-
-up: env
-	@docker compose up -d
-
-down:
-	@docker compose down
-
-ps:
-	@docker compose ps
-
-start:
-	@docker compose exec --user $(UID):$(GID) dev bash
-
-build: env
-	@docker compose up -d --build dev

paddle-1.1.10/docker-compose.override.yaml.tmp

@@ -1,6 +0,0 @@
-services:
-  dev:
-    volumes:
-      # This is your main working directory
-      # (lhs:rhs, lhs = workspace on physical machine : rhs = virtual machine)
-      - path_to_physical_directory/paddle_docker_workspace:/paddle_docker_workspace