[WIP] Add code from other repos.

.github/workflows/deploy.yaml

@@ -0,0 +1,43 @@
+# comment
+name: MyST GitHub Pages Deploy
+on:
+  push:
+    # Runs on pushes targeting the default branch
+    branches: [main, dev]
+env:
+  BASE_URL: /${{ github.event.repository.name }}
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+      - uses: actions/setup-node@v3
+        with:
+          node-version: 18.x
+      - name: Install MyST Markdown
+        run: npm install -g mystmd
+      - name: Build HTML Assets
+        run: myst build --html
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: "./_build/html"
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

.gitignore

@@ -0,0 +1,159 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+\.ipynb_checkpoints/
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# exclude data from source control by default
+datasets/*
+!datasets/.gitkeep
+*.npz
+\outputs
+\multirun
+**/outputs/*
+**/multirun/*
+\wandb/
+\checkpoints/
+notebooks/*.gif
+*.mp4
+*.png
+*.nc
+*.pickle
+*.pkl
+*.ckpt
+\lightning_logs/
+*.nc
+*.zarr
+*.npy
+*credentials.*
+*.pth
+\.idea/
+.DS_Store
+.vscode/settings.json
+\jbook/_build/
+\_build/
+*.keras

Makefile

@@ -0,0 +1,71 @@
+.PHONY: help install_mamba install_macos install_linux update_macos update_linux
+.DEFAULT_GOAL = help
+
+PYTHON = python
+VERSION = 3.8
+NAME = py_name
+ROOT = ./
+PIP = pip
+CONDA = conda
+SHELL = bash
+PKGROOT = nerf4ssh
+TESTS = ${PKGROOT}/nerf4ssh
+ENVS = ${PKGROOT}/environments
+
+help:	## Display this help
+	@awk 'BEGIN {FS = ":.*##"; printf "\nUsage:\n  make \033[36m\033[0m\n"} /^[a-zA-Z_-]+:.*?##/ { printf "  \033[36m%-15s\033[0m %s\n", $$1, $$2 } /^##@/ { printf "\n\033[1m%s\033[0m\n", substr($$0, 5) } ' $(MAKEFILE_LIST)
+
+
+
+##@ Installation
+install_mamba: ## Install mamba in base environment
+	conda install mamba -n base
+
+install_macos: ## Install conda env in MACOS
+	mamba env create -f ${ENVS}/macos.yaml
+
+install_linux: ## Install conda env in Linux
+	mamba env create -f ${ENVS}/linux.yaml
+
+update_macos: ## Update conda env in MACOS
+	mamba env update -f ${ENVS}/macos.yaml
+
+update_linux: ## Update conda env in linux
+	mamba env update -f ${ENVS}/linux.yaml
+
+install_precommit: ## Install precommit tools
+	mamba install pre-commit -c conda-forge
+	pre-commit install
+
+##@ Formatting
+black:  ## Format code in-place using black.
+	black ${PKGROOT}/ ${TESTS} -l 79 .
+
+isort:  ## Format imports in-place using isort.
+	isort ${PKGROOT}/ ${TESTS}
+
+format: ## Code styling - black, isort
+		black ${PKGROOT}/ ${TESTS} -l 79 .
+		@printf "\033[1;34mBlack passes!\033[0m\n\n"
+		isort ${PKGROOT}/ ${TESTS}
+		@printf "\033[1;34misort passes!\033[0m\n\n"
+
+##@ Testing
+test:  ## Test code using pytest.
+	@printf "\033[1;34mRunning tests with pytest...\033[0m\n\n"
+	pytest -v ${PKGROOT}/ ${TESTS}
+	@printf "\033[1;34mPyTest passes!\033[0m\n\n"
+
+##@ JupyterBook
+jb_build: ## Build Jupyterbook
+	rm -rf docs/_build/
+	jupyter-book build jbook --all
+
+jb_clean: ## Clean JupyterBook
+	jupyter-book clean jbook
+
+jb_publish: ## Clean JupyterBook
+	ghp-import -n -p -f _build/html
+
+run_versioneer: ## run the versioneer software
+	versioneer install --vendor

README.md

@@ -16,25 +16,45 @@ cd nerf4ssh
 mamba env create -f environments/linux.yaml
 ```
 
+### `pip`
+
+```bash
+pip install "git+https://github.com/jejjohnson/nerf4ssh.git"
+```
+
+### `poetry`
+
+```bash
+git clone https://github.com/jejjohnson/nerf4ssh.git
+cd nerf4ssh
+mamba create -n nerf4ssh python=3.10 poetry
+poetry install
+```
+
 
 ## External Packages
 
 I use quite a few of external packages that I've relegated to their own repo.
 
-**Neural Fields** - This package has all of the NerF algorithms I use for the experiments.
+**Neural Fields**
+
+I use the [`eqx-nerf`](https://github.com/jejjohnson/eqx-nerf) package has all of the NerF algorithms.
 
 ```bash
 pip install "git+https://github.com/jejjohnson/eqx-nerf.git"
 ```
 
-**Trainer** - This package has the NN Trainer and logging that I use for this experiment.
+**Trainer**
+
+I use the [`eqx-trainer`](https://github.com/jejjohnson/eqx-trainer) package for the NN Trainer and logging.
 
 ```bash
 pip install "git+https://github.com/jejjohnson/eqx-trainer.git"
 ```
 
+**OceanBench**
 
-**OceanBench** - This package has the datasets and metrics that I use for this paper.
+I use the [`OceanBench`](+https://github.com/jejjohnson/oceanbench) framework for the SSH datasets and metrics.
 
 ```bash
 brew install g++ cmake eigen boost gsl

_toc.yml

@@ -0,0 +1,35 @@
+# Table of Contents
+#
+# Myst will respect:
+# 1. New pages
+#      - file: relative/path/to/page
+# 2. New sections without an associated page
+#      - title: Folder Title
+#        sections: ...
+# 3. New sections with an associated page
+#      - file: relative/path/to/page
+#        sections: ...
+#
+# Note: Titles defined on pages here are not recognized.
+#
+# This spec is based on the JupyterBook table of contents.
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: content/overview
+chapters:
+  - title: Paper
+    sections:
+      - file: content/paper/1_introduction
+      - file: content/paper/2_methods
+      - file: content/paper/3_exp1_toy
+      - file: content/paper/4_exp2_osse
+      - file: content/paper/5_exp3_ose
+      - file: content/paper/6_conclusions
+  - title: Tutorials
+    sections:
+      - file: content/tutorials/1.1_naive_nerfs
+      - file: content/tutorials/1.2_spatial
+      - file: content/tutorials/1.3_spatiotemporal
+      - file: content/tutorials/2.1_osse_nadir
+      - file: content/tutorials/2.2_osse_nadirswot

config/logger/wandb.yaml

@@ -0,0 +1,10 @@
+_target_: pytorch_lightning.loggers.WandbLogger
+mode: "offline"
+save_dir: "/gpfsscratch/rech/cli/uvo53rl"
+entity: "ige"
+project: "jax4eo"
+id: null
+prefix: ""
+group: ""
+tags: []
+job_type: ""

config/lr_scheduler/default.yaml

@@ -0,0 +1 @@
+scheduler: null

config/lr_scheduler/warmup_cosine.yaml

@@ -0,0 +1,6 @@
+scheduler:
+  _target_: optax.warmup_cosine_decay_schedule
+  init_value: 0
+  peak_value: 1e0
+  warmup_steps: 25
+  end_value: 1e-5

config/main.yaml

@@ -0,0 +1,12 @@
+# @package _global_
+
+defaults:
+  - _self_
+  - data: default.yaml
+  - domain: gulfstream.yaml
+  - experiment: ose_gf_2017.yaml
+  - model: siren.yaml
+  - optimizer: adam
+  - paths: default.yaml
+  - period: default.yaml
+  - preprocess: default.yaml