paddle 1.1.14__tar.gz → 1.1.16__tar.gz

{paddle-1.1.14 → paddle-1.1.16}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.14
+current_version = 1.1.16
 commit = True
 tag = True
 

paddle-1.1.16/PKG-INFO

@@ -0,0 +1,161 @@
+Metadata-Version: 2.4
+Name: paddle
+Version: 1.1.16
+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
+Project-URL: Issues, https://github.com/elijah-mullens/paddle/issues
+Author-email: Elijah Mullens <eem85@cornell.edu>, Cheng Li <chengcli@umich.edu>
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
+Requires-Dist: kintera>=1.1.5
+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'
+Description-Content-Type: text/markdown
+
+# Paddle
+
+Python Atmospheric Dynamics: Discovering and Learning about Exoplanets. An open-source, user-friendly Python version of [canoe](https://github.com/chengcli/canoe).
+
+## Test the package
+
+Testing the package can be done very easily by following the steps below. All we need is to create a python virtual environment, install the package, and run the test script.
+
+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
+   ```
+
+## Develop with Docker
+
+You may need to install Docker to compose up and install the package inside a container if your device or operating system does not support certain dependencies. Follow the instructions below to install docker and docker-compose plugin.
+
+1. Install docker with compose
+
+   ```bash
+   curl -fsSL https://get.docker.com | sudo sh
+   ```
+
+2. Start docker using the command below or open docker desktop if applicable.
+
+   ```bash
+   sudo systemctl start docker
+   ```
+
+After installing Docker, you can use the Makefile commands below to manage your docker containers from the terminal. By default, the container will mount the current directory to `/paddle` inside the container.
+
+> Mounting a local directory allows you to edit files on your local machine while running and testing the code inside the container; or use the container as a development environment and sync files to your local machine.
+
+If you want to change the mounted directory, you can create a `docker-compose.overrides.yml` file based on the provided `docker-compose.overrides.yml.tmp` template file.
+
+- Create a docker container
+
+  ```bash
+  make up
+  ```
+
+- Start a docker container (only if previously created)
+
+  ```bash
+  make start
+  ```
+
+- Terminate a docker container
+
+  ```bash
+  make down
+  ```
+
+- Build a new docker image (rarely used)
+
+  ```bash
+  make build
+  ```
+
+If you use VSCode, it is recommended to install extensions including [Remote Development](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.vscode-remote-extensionpack), [Dev Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers) and [Container Tools](https://marketplace.visualstudio.com/items?itemName=ms-azuretools.vscode-containers) for a better development experience within a container.
+
+1. Install the extensions mentioned above.
+2. Start the container using `make up` or `make start`.
+3. Open VSCode and click on the "Containers" icon on the left sidebar. Note that if you have too many extensions installed, the icon may be hidden under the "..." menu.
+
+   <img src="docs/_static/readme-extension.png" width="200" style="vertical-align: top;">
+   <img src="docs/_static/readme-attach.png" width="200" style="vertical-align: top;">
+
+4. Right click on the running container named `paddle` with a green triangle icon (indicating it is running), and select "Attach Visual Studio Code" (see above images). This will open a new VSCode window connected to the container.
+5. Open either the default folder `paddle` mounted from your local machine, or any custom workspace folder you have set up inside the `docker-compose.overrides.yml` file. Now you can start developing inside the container as if you were working on your local machine!
+
+   <img src="docs/_static/readme-open-folder.png" width="500" style="vertical-align: top;">
+
+## For Developers
+
+Follow the steps below to set up your development environment.
+
+1. Clone the repository
+
+   ```bash
+   https://github.com/elijah-mullens/paddle
+   ```
+
+2. Cache your github credential. This will prevent you from being prompted for your username and password every time you push changes to github.
+
+   ```bash
+   git config credential.helper 'cache --timeout=86400'
+   ```
+
+3. Create a python virtual environment.
+
+   ```bash
+   python -m venv .pyenv
+   ```
+
+4. Install paddle package
+
+   ```bash
+   # Install the package normally
+   pip install paddle
+
+   # [Alternatively] if you want to install in editable mode
+   pip install -e .
+   ```
+
+5. Install pre-commit hook. This will automatically format your code before each commit to ensure consistent code style.
+
+   ```bash
+   pip install pre-commit
+   pre-commit install
+   ```
+
+## Troubleshooting
+
+1. If you have Docker installed but do not have Docker Compose, remove your current Docker installation, which could be docker or docker.io, and re-install it following the guide provided in the [Develop with Docker](#develop-with-docker) section above.

paddle-1.1.16/README.md

@@ -0,0 +1,129 @@
+# Paddle
+
+Python Atmospheric Dynamics: Discovering and Learning about Exoplanets. An open-source, user-friendly Python version of [canoe](https://github.com/chengcli/canoe).
+
+## Test the package
+
+Testing the package can be done very easily by following the steps below. All we need is to create a python virtual environment, install the package, and run the test script.
+
+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
+   ```
+
+## Develop with Docker
+
+You may need to install Docker to compose up and install the package inside a container if your device or operating system does not support certain dependencies. Follow the instructions below to install docker and docker-compose plugin.
+
+1. Install docker with compose
+
+   ```bash
+   curl -fsSL https://get.docker.com | sudo sh
+   ```
+
+2. Start docker using the command below or open docker desktop if applicable.
+
+   ```bash
+   sudo systemctl start docker
+   ```
+
+After installing Docker, you can use the Makefile commands below to manage your docker containers from the terminal. By default, the container will mount the current directory to `/paddle` inside the container.
+
+> Mounting a local directory allows you to edit files on your local machine while running and testing the code inside the container; or use the container as a development environment and sync files to your local machine.
+
+If you want to change the mounted directory, you can create a `docker-compose.overrides.yml` file based on the provided `docker-compose.overrides.yml.tmp` template file.
+
+- Create a docker container
+
+  ```bash
+  make up
+  ```
+
+- Start a docker container (only if previously created)
+
+  ```bash
+  make start
+  ```
+
+- Terminate a docker container
+
+  ```bash
+  make down
+  ```
+
+- Build a new docker image (rarely used)
+
+  ```bash
+  make build
+  ```
+
+If you use VSCode, it is recommended to install extensions including [Remote Development](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.vscode-remote-extensionpack), [Dev Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers) and [Container Tools](https://marketplace.visualstudio.com/items?itemName=ms-azuretools.vscode-containers) for a better development experience within a container.
+
+1. Install the extensions mentioned above.
+2. Start the container using `make up` or `make start`.
+3. Open VSCode and click on the "Containers" icon on the left sidebar. Note that if you have too many extensions installed, the icon may be hidden under the "..." menu.
+
+   <img src="docs/_static/readme-extension.png" width="200" style="vertical-align: top;">
+   <img src="docs/_static/readme-attach.png" width="200" style="vertical-align: top;">
+
+4. Right click on the running container named `paddle` with a green triangle icon (indicating it is running), and select "Attach Visual Studio Code" (see above images). This will open a new VSCode window connected to the container.
+5. Open either the default folder `paddle` mounted from your local machine, or any custom workspace folder you have set up inside the `docker-compose.overrides.yml` file. Now you can start developing inside the container as if you were working on your local machine!
+
+   <img src="docs/_static/readme-open-folder.png" width="500" style="vertical-align: top;">
+
+## For Developers
+
+Follow the steps below to set up your development environment.
+
+1. Clone the repository
+
+   ```bash
+   https://github.com/elijah-mullens/paddle
+   ```
+
+2. Cache your github credential. This will prevent you from being prompted for your username and password every time you push changes to github.
+
+   ```bash
+   git config credential.helper 'cache --timeout=86400'
+   ```
+
+3. Create a python virtual environment.
+
+   ```bash
+   python -m venv .pyenv
+   ```
+
+4. Install paddle package
+
+   ```bash
+   # Install the package normally
+   pip install paddle
+
+   # [Alternatively] if you want to install in editable mode
+   pip install -e .
+   ```
+
+5. Install pre-commit hook. This will automatically format your code before each commit to ensure consistent code style.
+
+   ```bash
+   pip install pre-commit
+   pre-commit install
+   ```
+
+## Troubleshooting
+
+1. If you have Docker installed but do not have Docker Compose, remove your current Docker installation, which could be docker or docker.io, and re-install it following the guide provided in the [Develop with Docker](#develop-with-docker) section above.

{paddle-1.1.14 → paddle-1.1.16}/example_py_scripts/robert.yaml

@@ -15,7 +15,7 @@ geometry:
 distribute:
   backend: gloo
   layout: slab
-  nb2: 4
+  nb2: 1
   nb3: 1
   verbose: false
 

{paddle-1.1.14 → paddle-1.1.16}/example_py_scripts/test_saturn_adiabat.py

@@ -14,7 +14,8 @@ from pathlib import Path
 
 def setup_saturn_profile():
     # path = resources.files("paddle") / "data" / "saturn1d.yaml"
-    path = Path("data") / "saturn1d.yaml"
+    # path = Path("data") / "saturn1d.yaml"
+    path = "saturn1d.yaml"
     print(f"Reading input file: {path}")
 
     op_block = MeshBlockOptions.from_yaml(str(path))

{paddle-1.1.14 → paddle-1.1.16}/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__ = "1.1.14"
+__version__ = "1.1.16"

{paddle-1.1.14 → paddle-1.1.16}/paddle/crm.py

@@ -4,7 +4,6 @@ import time
 import kintera
 import numpy as np
 from snapy import (
-    index,
     MeshBlockOptions,
     MeshBlock,
     OutputOptions,
@@ -16,6 +15,7 @@ from kintera import (
     KineticsOptions,
     Kinetics,
 )
+from snapy import kIDN, kICY
 
 if __name__ == "__main__":
     # input file
@@ -59,7 +59,7 @@ if __name__ == "__main__":
 
         if count % 1 == 0:
             print(f"count = {count}, dt = {dt}, time = {current_time}")
-            print("mass = ", u[interior][index.idn].sum())
+            print("mass = ", u[interior][kIDN].sum())
 
             for out in outs:
                 out.increment_file_number()
@@ -70,7 +70,7 @@ if __name__ == "__main__":
             block.forward(dt, stage)
 
         # evolve kinetics
-        u[index.icy :] += evolve_kinetics(block, kinet, thermo_x)
+        u[kICY:] += evolve_kinetics(block, kinet, thermo_x)
 
         current_time += dt
         count += 1

{paddle-1.1.14 → paddle-1.1.16}/paddle/evolve_kinetics.py

@@ -1,6 +1,7 @@
 import torch
 import snapy
 import kintera
+from snapy import kIDN, kIPR, kICY
 
 
 def evolve_kinetics(
@@ -27,8 +28,8 @@ def evolve_kinetics(
     thermo_y = block.module("hydro.eos.thermo")
 
     temp = eos.compute("W->T", (hydro_w,))
-    pres = hydro_w[snapy.index.ipr]
-    xfrac = thermo_y.compute("Y->X", (hydro_w[snapy.index.icy :],))
+    pres = hydro_w[kIPR]
+    xfrac = thermo_y.compute("Y->X", (hydro_w[kICY:],))
     conc = thermo_x.compute("TPX->V", (temp, pres, xfrac))
     cp_vol = thermo_x.compute("TV->cp", (temp, conc))
 

paddle-1.1.16/paddle/example_save.py

@@ -0,0 +1,22 @@
+import torch
+import types
+
+
+def save_tensors(tensor_map: dict[str, torch.Tensor], filename: str):
+    class TensorModule(torch.nn.Module):
+        def __init__(self, tensors):
+            super().__init__()
+            for name, tensor in tensors.items():
+                self.register_buffer(name, tensor)
+
+    module = TensorModule(tensor_map)
+    scripted = torch.jit.script(module)  # Needed for LibTorch compatibility
+    scripted.save(filename)
+
+
+if __name__ == "__main__":
+    tensors = {
+        "foo": torch.randn(3, 4),
+        "bar": torch.randn(5, 6),
+    }
+    save_tensors(tensors, "foo_bar.pt")

{paddle-1.1.14 → paddle-1.1.16}/paddle/find_init_params.py

@@ -1,6 +1,7 @@
 from scipy.interpolate import interp1d
 import snapy
 import numpy as np
+from snapy import kIPR
 
 from .setup_profile import setup_profile
 
@@ -46,7 +47,7 @@ def find_init_params(
         temp = eos.compute("W->T", (w,)).squeeze()
 
         # calculate 1D pressure
-        pres = w[snapy.index.ipr, ...].squeeze()
+        pres = w[kIPR, ...].squeeze()
 
         # temperature function
         t_func = interp1d(

{paddle-1.1.14 → paddle-1.1.16}/paddle/setup_profile.py

@@ -3,6 +3,7 @@ from typing import Tuple
 import torch
 import snapy
 import kintera
+from snapy import kIDN, kIPR, kICY
 
 
 def integrate_neutral(
@@ -248,9 +249,9 @@ def setup_profile(
             xfrac /= xfrac.sum(dim=-1, keepdim=True)
         conc = thermo_x.compute("TPX->V", [temp, pres, xfrac])
 
-        w[snapy.index.ipr, ..., i] = pres
-        w[snapy.index.idn, ..., i] = thermo_x.compute("V->D", [conc])
-        w[snapy.index.icy :, ..., i] = thermo_x.compute("X->Y", [xfrac])
+        w[kIPR, ..., i] = pres
+        w[kIDN, ..., i] = thermo_x.compute("V->D", [conc])
+        w[kICY:, ..., i] = thermo_x.compute("X->Y", [xfrac])
 
         dz = coord.buffer("dx1f")[i]
         if method.split("-")[0] == "dry":
@@ -279,7 +280,7 @@ def setup_profile(
         dz = coord.buffer("dx1f")[i]
         pres *= torch.exp(-grav * mu * dz / (kintera.constants.Rgas * temp))
         conc = thermo_x.compute("TPX->V", [temp, pres, xfrac])
-        w[snapy.index.ipr, ..., i] = pres
-        w[snapy.index.idn, ..., i] = thermo_x.compute("V->D", [conc])
-        w[snapy.index.icy :, ..., i] = thermo_x.compute("X->Y", [xfrac])
+        w[kIPR, ..., i] = pres
+        w[kIDN, ..., i] = thermo_x.compute("V->D", [conc])
+        w[kICY:, ..., i] = thermo_x.compute("X->Y", [xfrac])
     return w

{paddle-1.1.14 → paddle-1.1.16}/paddle/write_profile.py

@@ -6,6 +6,7 @@ import numpy as np
 import torch
 import kintera
 import snapy
+from snapy import kIPR, kICY
 
 
 def write_profile(
@@ -47,7 +48,7 @@ def write_profile(
         raise ValueError("hydro_w must have shape (N, 1, 1, L).")
 
     # calculate a height grid
-    pres = hydro_w[snapy.index.ipr, ...].squeeze() / 1.0e5  # Pa -> bar
+    pres = hydro_w[kIPR, ...].squeeze() / 1.0e5  # Pa -> bar
     zlev_func = interp1d(
         pres.log().cpu().numpy(),
         coord.buffer("x1v").cpu().numpy(),
@@ -61,7 +62,7 @@ def write_profile(
     temp = eos.compute("W->T", (hydro_w,)).squeeze()
 
     # calculate mole fractions
-    xfrac = thermo_y.compute("Y->X", (hydro_w[snapy.index.icy :, ...],)).squeeze()
+    xfrac = thermo_y.compute("Y->X", (hydro_w[kICY:, ...],)).squeeze()
 
     # calculate heat capacity
     conc = thermo_x.compute("TPX->V", (temp, pres * 1.0e5, xfrac))

{paddle-1.1.14 → paddle-1.1.16}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "paddle"
-version = "1.1.14"
+version = "1.1.16"
 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-1.1.14/PKG-INFO

@@ -1,115 +0,0 @@
-Metadata-Version: 2.4
-Name: paddle
-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
-Project-URL: Issues, https://github.com/elijah-mullens/paddle/issues
-Author-email: Elijah Mullens <eem85@cornell.edu>, Cheng Li <chengcli@umich.edu>
-License-File: LICENSE
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Science/Research
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Topic :: Scientific/Engineering :: Astronomy
-Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
-Classifier: Topic :: Scientific/Engineering :: Physics
-Requires-Python: >=3.9
-Requires-Dist: kintera>=1.1.5
-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'
-Description-Content-Type: text/markdown
-
-# 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'
-```
-
-### Create a python virtual environment
-```bash
-python -m venv .pyenv
-```
-
-### 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-1.1.14/README.md

@@ -1,83 +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
-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'
-```
-
-### Create a python virtual environment
-```bash
-python -m venv .pyenv
-```
-
-### 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